Mercurial > repos > rnateam > rbpbench
changeset 0:7dd2835ce566 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench commit 0e21bd630200c1f199db8ba5d83b81d4214fc59f
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/batch_table_wrapper.py Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,242 @@ +#!/usr/bin/env python3 + +import argparse +import os +import re +import subprocess + + +############################################################################### + +def setup_argument_parser(): + """Setup argparse parser.""" + help_description = """ + Python wrapper for RBPBench Galaxy wrapper to work with collections of + input BED files (i.e. to process them with rbpbench batch). + """ + # Define argument parser. + p = argparse.ArgumentParser(add_help=False, + prog="batch_table_wrapper.py", + description=help_description, + formatter_class=argparse.MetavarTypeHelpFormatter) + + # Required arguments. + p.add_argument("-h", "--help", + action="help", + help="Print help message") + p.add_argument("--table", + dest="in_table", + type=str, + metavar='str', + required=True, + help="Input table file with data ID, method ID, RBP ID and file name (Galaxy element identifier in dataset collection) for each to be processed dataset by rbpbench batch") + p.add_argument("--paths", + dest="in_paths", + type=str, + metavar='str', + nargs='+', + required=True, + help="List of Galaxy BED file paths (--files path1 path2 .. )") + p.add_argument("--ids", + dest="in_ids", + type=str, + metavar='str', + nargs='+', + required=True, + help="List of Galaxy element identifiers, equal to the BED dataset names in the dataset collection (--ids id1 id2 .. )") + p.add_argument("--genome", + dest="in_genome", + type=str, + metavar='str', + required=True, + help="Genomic sequences file (currently supported formats: FASTA)") + p.add_argument("--out", + dest="out_folder", + type=str, + metavar='str', + required=True, + help="Batch results output folder") + # Optional batch arguments. + p.add_argument("--ext", + dest="ext_up_down", + type=str, + metavar='str', + default="0", + help="Up- and downstream extension of --in sites in nucleotides (nt). Set e.g. --ext 30 for 30 nt on both sides, or --ext 20,10 for different up- and downstream extension (default: 0)") + p.add_argument("--motif-db", + dest="motif_db", + type=int, + default=1, + choices=[1, 2, 3], + help="Motif database to use. 1: human RBP motifs full (259 RBPs, 605 motifs, human_v0.1), 2: human RBP motifs full (low frequencies not rounded, human_v0.1_no_round), 3: human RBP motifs eCLIP (107 RBPs, 316 motifs, human_eclip_v0.1) (default: 1)") + p.add_argument("--fimo-nt-freqs", + dest="fimo_nt_freqs", + type=str, + metavar='str', + default=False, + help="Provide FIMO nucleotide frequencies (FIMO option: --bifile) file (default: use internal frequencies file optimized for human transcripts)") + p.add_argument("--fimo-pval", + dest="fimo_pval", + type=float, + metavar='float', + default=0.001, + help="FIMO p-value threshold (FIMO option: --thresh) (default: 0.001)") + p.add_argument("--bed-score-col", + dest="bed_score_col", + type=int, + metavar='int', + default=5, + help="--in BED score column used for p-value calculations. BED score can be e.g. log2 fold change or -log10 p-value of the region (default: 5)") + p.add_argument("--unstranded", + dest="unstranded", + default=False, + action="store_true", + help="Set if --in BED regions are NOT strand-specific, i.e., to look for motifs on both strands of the provided regions. Note that the two strands of a region will still be counted as one region (change with --unstranded-ct) (default: False)") + p.add_argument("--unstranded-ct", + dest="unstranded_ct", + default=False, + action="store_true", + help="Count each --in region twice for RBP hit statistics when --unstranded is enabled. By default, two strands of one region are counted as one region for RBP hit statistics") + return p + + +############################################################################### + +if __name__ == '__main__': + + parser = setup_argument_parser() + args = parser.parse_args() + + assert os.path.exists(args.in_table), "--table file \"%s\" not found" % (args.in_file) + assert os.path.exists(args.in_genome), "--genome file \"%s\" not found" % (args.in_genome) + + c_paths = len(args.in_paths) + c_ids = len(args.in_ids) + assert c_paths == c_ids, "given # paths (--paths) != # ids (--ids) (%i != %i). Please provide one ID for each path" % (c_paths, c_ids) + + """ + Check given paths and IDs. + + """ + + # Paths. + paths_dic = {} + paths_list = [] + for path in args.in_paths: + assert os.path.exists(path), "--paths %s file not found" % (path) + if path not in paths_dic: + paths_dic[path] = 1 + else: + assert False, "--paths %s given > 1. Please provide unique paths" % (path) + paths_list.append(path) + + # IDs + ids_dic = {} + ids_list = [] + for id in args.in_ids: + if id not in ids_dic: + ids_dic[id] = 1 + else: + assert False, "--ids \"%s\" given > 1. Please provide unique element identifiers (dataset names) inside the dataset collection, in order to unambiguously assign element ID to file path" % (id) + ids_list.append(id) + + id2path_dic = {} + for idx, id in enumerate(ids_list): + path = paths_list[idx] + id2path_dic[id] = path + + """ + Read in table. + + Column format: + rbp_id method_id data_id dataset_name + + """ + + comb_ids_dic = {} + id_collect_dic = {} + id_collect_dic["rbp_id"] = [] + id_collect_dic["method_id"] = [] + id_collect_dic["data_id"] = [] + id_collect_dic["set_name"] = [] + id_collect_dic["path"] = [] # Galaxy file path. + + print("Read in --table ... ") + + with open(args.in_table) as f: + for line in f: + + if re.search("^#", line): + continue + + cols = line.strip().split("\t") + + assert len(cols) == 4, "line in --table with # cols != 4 (%i) encountered:%s" % (len(cols), line) + + rbp_id = cols[0] + method_id = cols[1] + data_id = cols[2] + set_name = cols[3] + + if rbp_id == "rbp_id": + continue + + comb_id = "%s,%s,%s,%s" % (rbp_id, method_id, data_id, set_name) + + if comb_id not in comb_ids_dic: + comb_ids_dic[comb_id] = 1 + else: + assert False, "data combination (\"%s\") appears > 1 in --table file. Please provide unique combinations for rbpbench batch calculation" % (comb_id) + + assert set_name in ids_dic, "given dataset name \"%s\" from --table not part of given --ids. Please provide dataset names present in dataset collection" % (set_name) + + id_collect_dic["rbp_id"].append(rbp_id) + id_collect_dic["method_id"].append(method_id) + id_collect_dic["data_id"].append(data_id) + id_collect_dic["set_name"].append(set_name) + id_collect_dic["path"].append(id2path_dic[set_name]) + + f.closed + + assert id_collect_dic["rbp_id"], "nothing read in from --table. Please provide non-empty table in correct format (columns: rbp_id method_id data_id dataset_name)" + + """ + Construct RBPBench batch call. + + """ + + batch_call = "rbpbench batch" + batch_call += " --out %s" % (args.out_folder) + batch_call += " --genome %s" % (args.in_genome) + batch_call += " --ext %s" % (args.ext_up_down) + batch_call += " --motif-db %i" % (args.motif_db) + if args.fimo_nt_freqs: + batch_call += " --fimo-nt-freqs %s" % (args.fimo_nt_freqs) + batch_call += " --fimo-pval %s" % (str(args.fimo_pval)) + batch_call += " --bed-score-col %i" % (args.bed_score_col) + if args.unstranded: + batch_call += " --unstranded" + if args.unstranded_ct: + batch_call += " --unstranded-ct" + + rbp_ids = (" ").join(id_collect_dic["rbp_id"]) + method_ids = (" ").join(id_collect_dic["method_id"]) + data_ids = (" ").join(id_collect_dic["data_id"]) + paths = (" ").join(id_collect_dic["path"]) + + batch_call += " --rbp-list %s" % (rbp_ids) + batch_call += " --method-list %s" % (method_ids) + batch_call += " --data-list %s" % (data_ids) + batch_call += " --bed %s" % (paths) + + """ + Execute RBPBench batch call. + """ + + print("") + print("EXECUTING CALL:\n%s" % (batch_call)) + output = subprocess.getoutput(batch_call) + print("") + print("RUN OUTPUT:\n%s" % (output)) + print("") + print("DONE.")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,40 @@ +<macros> + <token name="@TOOL_VERSION@">0.7</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@profile@">22.05</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rbpbench</requirement> + <requirement type="package" version="5.5.4">meme</requirement> + </requirements> + </xml> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">rbpbench</xref> + </xrefs> + </xml> + <!--xml name="citations"> + <citations> + <citation type="doi"></citation> + </citations> + </xml--> + <token name="@PREPARE_REF@"><![CDATA[ + ln -s -f + #if str($action_type.reference_genome.reference_genome_selector) == "history" + '$action_type.reference_genome.history_genome' + #else + '$action_type.reference_genome.builtin_genome.fields.path' + #end if + reference.fa && + ]]></token> + <token name="@COMMON_PARAMS@"><![CDATA[ + --ext $action_type.search_options.search_ext + --fimo-pval $action_type.search_options.search_fimo_pval + --bed-score-col $action_type.search_options.search_bed_score_col + $action_type.search_options.search_unstranded + $action_type.search_options.search_unstranded_ct + #if $action_type.search_options.fimo_nt_freqs_file: + --fimo-nt-freqs '$action_type.search_options.fimo_nt_freqs_file' + #end if + ]]></token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbpbench.xml Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,1003 @@ +<tool id="rbpbench" name="RBPBench" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@"> + + <description>- Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + + <command detect_errors="exit_code"><![CDATA[ + #if $action_type.action_type_selector == 'search_motifs': + @PREPARE_REF@ + rbpbench search + --in '$action_type.search_bed_file' + --out ./ + --genome reference.fa + --method-id '$action_type.search_method_id' + --data-id '$action_type.search_data_id' + --rbps + #if str($action_type.select_db.select_db_selector) == "default_db": + #if str($action_type.select_db.select_rbps.select_rbps_selector) == "list_db_rbps": + #if str($action_type.select_db.select_rbps.database) != "None": + #for $rbp_id in str($action_type.select_db.select_rbps.database).split(','): + $rbp_id + #end for + #end if + #else: + ALL + #end if + #else: + $action_type.select_db.custom_db_rbp_ids_list + #end if + + #if str($action_type.user_rbp.user_rbp_selector) == "sequence": + USER + --user-rbp-id $action_type.user_rbp.seq_rbp_id + --user-meme-xml '$action_type.user_rbp.meme_motifs_xml' + #elif str($action_type.user_rbp.user_rbp_selector) == "structure": + USER + --user-rbp-id $action_type.user_rbp.str_rbp_id + --user-cm '$action_type.user_rbp.cm_model_file' + #end if + + #if str($action_type.select_db.select_db_selector) == "custom_db": + --custom-db-id $action_type.select_db.custom_db_id + --custom-db-info $action_type.select_db.custom_db_info_file + #if $action_type.select_db.custom_db_meme_xml_file: + --custom-db-meme-xml '$action_type.select_db.custom_db_meme_xml_file' + #end if + #if $action_type.select_db.custom_db_cm_model_file: + --custom-db-cm '$action_type.select_db.custom_db_cm_model_file' + #end if + #end if + @COMMON_PARAMS@ + #if $action_type.report_plotting_options.set_rbp_id: + --set-rbp-id '$action_type.report_plotting_options.set_rbp_id' + #end if + --motif-distance-plot-range $action_type.report_plotting_options.motif_distance_plot_range + --motif-min-pair-count $action_type.report_plotting_options.motif_min_pair_count + --rbp-min-pair-count $action_type.report_plotting_options.rbp_min_pair_count + #if $action_type.report_plotting_options.gtf_file: + --gtf '$action_type.report_plotting_options.gtf_file' + #end if + #if $action_type.report_plotting_options.tr_list_file: + --tr-list '$action_type.report_plotting_options.tr_list_file' + #end if + #if $action_type.report_plotting_options.list_tr_biotypes: + --tr-types '$action_type.report_plotting_options.list_tr_biotypes' + #end if + --upset-plot-min-degree $action_type.report_plotting_options.upset_plot_min_degree + #if $action_type.report_plotting_options.upset_plot_max_degree: + --upset-plot-max-degree '$action_type.report_plotting_options.upset_plot_max_degree' + #end if + --upset-plot-min-subset-size $action_type.report_plotting_options.upset_plot_min_subset_size + + $action_type.search_output_options.search_report + $action_type.search_output_options.search_plot_motifs + + #if $action_type.report_plotting_options.store_sort_js_in_html: + --sort-js-mode 3 + #else: + --sort-js-mode 2 + #end if + #if $action_type.report_plotting_options.plotly_js_source == 1: + #if $action_type.report_plotting_options.plotly_plot_code_in_html: + --plotly-js-mode 6 + #else: + --plotly-js-mode 3 + #end if + #elif $action_type.report_plotting_options.plotly_js_source == 2: + #if $action_type.report_plotting_options.plotly_plot_code_in_html: + --plotly-js-mode 5 + #else: + --plotly-js-mode 1 + #end if + #else: + #if $action_type.report_plotting_options.plotly_plot_code_in_html: + --plotly-js-mode 7 + #else: + --plotly-js-mode 4 + #end if + #end if + + #if $action_type.search_output_options.search_report: + && + sed -i 's/html_report_plots\///g' ./report.rbpbench_search.html + && + cp ./report.rbpbench_search.html $search_report_html_file + && + mkdir '$search_report_html_file.extra_files_path' + && + cp -r ./html_report_plots/* '$search_report_html_file.extra_files_path' + #end if + + #if $action_type.search_output_options.search_plot_motifs: + && + sed -i 's/html_motif_plots\///g' ./motif_plots.rbpbench_search.html + && + cp ./motif_plots.rbpbench_search.html $motif_plots_html_file + && + mkdir '$motif_plots_html_file.extra_files_path' + && + cp -r ./html_motif_plots/* '$motif_plots_html_file.extra_files_path' + #end if + + + #elif $action_type.action_type_selector == 'batch_search_motifs': + @PREPARE_REF@ + rbpbench batch + --out ./ + --genome reference.fa + --bed + #for $i in $action_type.dataset_inputs: + $i.dataset_bed_file + #end for + --rbp-list + #for $i in $action_type.dataset_inputs: + $i.dataset_rbp_id + #end for + --data-list + #for $i in $action_type.dataset_inputs: + $i.dataset_data_id + #end for + --method-list + #for $i in $action_type.dataset_inputs: + $i.dataset_method_id + #end for + @COMMON_PARAMS@ + + #elif $action_type.action_type_selector == 'batch_table_search_motifs': + @PREPARE_REF@ + batch_table_wrapper_rbpbench.py + --out ./ + --genome reference.fa + --table '$action_type.batch_table_file' + --paths + #for $i in $action_type.batch_table_bed_collection: + $i + #end for + --ids + #for $i in $action_type.batch_table_bed_collection: + $i.element_identifier + #end for + @COMMON_PARAMS@ + + #elif $action_type.action_type_selector == 'plot_nt_dist': + @PREPARE_REF@ + rbpbench dist + --in '$action_type.dist_bed_file' + --out ./ + --genome reference.fa + --cp-mode $action_type.dist_options.dist_cp_mode + --ext $action_type.dist_options.dist_ext + $action_type.dist_options.dist_plot_pdf + + + #elif $action_type.action_type_selector == 'compare_search_results': + rbpbench compare + --in + #for $in_file in $action_type.input_tables: + $in_file + #end for + --out ./ + #if $action_type.compare_output_options.store_sort_js_in_html: + --sort-js-mode 3 + #else: + --sort-js-mode 2 + #end if + + && + sed -i 's/html_report_plots\///g' ./report.rbpbench_compare.html + && + cp ./report.rbpbench_compare.html $compare_report_html_file + && + mkdir '$compare_report_html_file.extra_files_path' + && + cp -r ./html_report_plots/* '$compare_report_html_file.extra_files_path' + + #end if + + ]]></command> + + <inputs> + + <conditional name="action_type"> + + <param name="action_type_selector" type="select" label="Select RBPBench program mode"> + <option value="search_motifs" selected="true">Search RBP binding motifs in genomic regions</option> + <option value="batch_search_motifs">Search RBP binding motifs in genomic regions (multiple inputs)</option> + <option value="batch_table_search_motifs">Search RBP binding motifs in genomic regions (data collection input)</option> + <option value="plot_nt_dist">Plot nucleotide distribution at genomic positions</option> + <option value="compare_search_results">Compare different search results</option> + </param> + + <!-- rbpbench search --> + <when value="search_motifs"> + <param name="search_bed_file" type="data" format="bed" label="Genomic regions BED file" + help="Genomic regions (e.g. RBP binding sites) in BED format (>= 6-columns) for RBP binding motif search"/> + <conditional name="reference_genome"> + <param label="Select reference genome sequence (according to provided BED file)" name="reference_genome_selector" type="select"> + <option selected="True" value="builtin">Select built-in genome sequence</option> + <option value="history">Select genome sequence from history</option> + </param> + <when value="builtin"> + <param label="Select built-in genome sequence" name="builtin_genome" type="select"> + <options from_data_table="fasta_indexes"> + <filter column="2" type="sort_by" /> + <validator message="No genomes are available for the selected input dataset" type="no_options" /> + </options> + </param> + </when> + <when value="history"> + <param format="fasta" type="data" name="history_genome" label="Select genome sequence in FASTA format from history"/> + </when> + </conditional> + <conditional name="select_db"> + <param name="select_db_selector" type="select" label="Select RBP binding motif database"> + <option selected="True" value="default_db" >Human motif database with 259 RBPs and 605 RBP binding motifs (catrapid.omics.v2.1.human.6plus)</option> + <option value="custom_db" >Provide a custom motif database</option> + </param> + <when value="default_db"> + + <conditional name="select_rbps"> + <param name="select_rbps_selector" type="select" label="Select RBPs for motif search"> + <option selected="True" value="list_db_rbps" >Select individual RBPs </option> + <option value="all_db_rbps" >Select all 259 RBPs</option> + </param> + <when value="list_db_rbps"> + <param name="database" label="Select RBPs" type="select" multiple="true"> + <options from_data_table='rbp_ids_table' /> + </param> + </when> + <when value="all_db_rbps"> + <!-- do nothing --> + </when> + </conditional> + </when> + <when value="custom_db"> + <param type="text" name="custom_db_id" value="custom_db_id" + label="Custom motif database ID" + help="Set ID / name for provided custom motif database (default: custom_db_id)"/> + + <param type="data" format="txt,tabular" name="custom_db_info_file" + label="Custom motif database info table file" + help="Provide custom motif database info table file containing RBP ID -> motif ID -> motif type assignments. The motif IDs must correspond to the provided custom MEME / DREME XML and/or covariance models file(s)."/> + + <param type="data" format="memexml" name="custom_db_meme_xml_file" optional="True" + label="Custom motif database MEME / DREME XML file" + help="Provide custom motif database MEME / DREME XML file containing sequence motifs"/> + + <param type="data" format="cm" name="custom_db_cm_model_file" optional="True" + label="Custom motif database covariance models file" + help="Provide custom motif database covariance models file containing structure motif(s) (i.e., covariance model(s))"/> + + <param name="custom_db_rbp_ids_list" type="text" value="RBP1 RBP2 RBP3" + label="Specify RBP IDs from custom motif database" + help="Provide list of RBP IDs found in custom motif database to use for motif search. This can be a single ID, as well as several (separated by spaces, as in the example). To search using all RBPs in the custom database, simply type ALL."/> + </when> + </conditional> + + <conditional name="user_rbp"> + <param label="Add user-supplied motifs" name="user_rbp_selector" type="select"> + <option selected="True" value="no">No</option> + <option value="sequence">Yes (MEME/DREME XML based sequence motif(s))</option> + <option value="structure">Yes (Covariance model based structure motif(s))</option> + </param> + <when value="sequence"> + <param format="memexml" type="data" name="meme_motifs_xml" + label="DREME or MEME motifs XML file" + help="DREME or MEME output XML file containing sequence motif(s)"/> + <param type="text" name="seq_rbp_id" value="User_RBP" + label="RBP ID" + help="RBP ID (RBP name) for provided sequence motif(s). Make sure to provide user RBP IDs and motif IDs that are different from selected database RBP and motif IDs."/> + </when> + <when value="structure"> + <param format="cm" type="data" name="cm_model_file" + label="Covariance models file" + help="Covariance models file containing structure motif(s)"/> + <param type="text" name="str_rbp_id" value="User_RBP" + label="RBP ID" + help="RBP ID (RBP name) for provided structure motif(s). Make sure to provide user RBP IDs and motif IDs that are different from selected database RBP and motif IDs."/> + </when> + <when value="no"> + <!-- do nothing --> + </when> + </conditional> + + <param type="text" name="search_method_id" value="method_id" + label="Method ID" + help="Method ID which can be used to describe the peak calling method (e.g. clipper_idr). This ID (together with data ID and set RBP ID(s)) defines which search results get compared in RBPBench's comparison mode (see Help below for more details)."/> + <param type="text" name="search_data_id" value="data_id" + label="Data ID" + help="Data ID which can be used to describe from which cell type and/or CLIP-seq protocol the data originates (e.g. k562_eclip or pum2_k562_eclip). This ID (together with method ID and set RBP ID(s)) defines which search results get compared in RBPBench's comparison mode (see Help below for more details)."/> + + <section name="search_options" title="Motif search settings"> + <param name="search_ext" type="text" value="0" + label="Up- and downstream extension of genomic regions" + help='Up- and downstream extension of genomic regions in nucleotides (nt). E.g. set to "30" to extend 30 nt on both sides, or "20,10" for different up- and downstream extension (default: 0)'/> + <param name="search_fimo_pval" type="float" value="0.001" + label="FIMO p-value threshold" + help='FIMO p-value threshold (FIMO option: --thresh) for reporting motif hits (default: 0.001)'/> + <param name="search_bed_score_col" type="integer" value="5" + label="BED score column used for p-value calculations" + help="Score column of genomic regions BED file used for p-value calculations. BED score can be e.g. log2 fold change or -log10 p-value of the region (default: 5)"/> + <param name="search_unstranded" label="Treat genomic regions in BED file as NOT strand-specific" type="boolean" + truevalue="--unstranded" falsevalue="" checked="False" + help="Set if genomic regions in BED file are NOT strand-specific, i.e., to look for motifs on both strands of the provided regions. Note that the two strands of a region will still be counted as one region (change with option below) (default: False)"/> + <param name="search_unstranded_ct" label="Count each genomic region twice for RBP hit statistics" type="boolean" + truevalue="--unstranded-ct" falsevalue="" checked="False" + help="Count each genomic region twice for RBP hit statistics when non-strand-specific option above is enabled (default: False)"/> + <param format="txt" type="data" name="fimo_nt_freqs_file" optional="True" + label="Provide FIMO nucleotide frequencies file" + help="Provide FIMO nucleotide frequencies (FIMO option: --bifile) file. By default, an internal frequencies file optimized for human transcripts is used"/> + </section> + + <section name="report_plotting_options" title="HTML report options"> + + <param format="gtf" type="data" name="gtf_file" optional="True" + label="GTF file to add genomic annotations to input regions" + help="Provide GTF file with genomic annotations to add to HTML report plots (e.g. from GENCODE or Ensembl). By default, the most prominent transcripts will be extracted and used for functional annotation. Alternatively, provide a list of expressed transcripts via --tr-list option (together with --gtf containing the transcripts). Note that currently only features on standard chromosomes (1,2,..,X,Y,MT) are used for annotation"/> + <param format="txt" type="data" name="tr_list_file" optional="True" + label="Transcript IDs file" + help="Supply file with transcript IDs (one ID per row) to define which transcripts to use from GTF file for adding functional annotations to HTML report plots"/> + <param name="list_tr_biotypes" type="text" optional="True" + label="List of transcript biotypes" + help="List of transcript biotypes to consider from GTF file. By default an internal selection of transcript biotypes is used (in addition to intron, CDS, UTR, intergenic). Provide a list of IDs separated by spaces. Note that provided biotype IDs need to be in GTF file!"/> + + <param name="upset_plot_min_degree" type="integer" value="2" + label="Upset plot minimum degree parameter" + help="Upset plot minimum degree parameter for HTML report upset plot. This defines the minimum number of RBPs for a combination to be included (default: 2)"/> + <param name="upset_plot_max_degree" type="integer" value="" optional="True" + label="Upset plot maximum degree parameter" + help="Upset plot maximum degree parameter for HTML report upset plot. By default no maximum degree is set. Useful together with minimum degree to look at specific degrees (e.g. only 2, or between 2 and 3) (default: None)"/> + <param name="upset_plot_min_subset_size" type="integer" value="5" + label="Upset plot minimum subset size parameter" + help="Upset plot minimum subset size parameter for HTML report upset plot. This defines the minimum number of hits for a specific RBP combination to be included (default: 5)"/> + + <param type="text" name="set_rbp_id" optional="True" + label="Set reference RBP ID for plotting motif distances" + help="Set reference RBP ID to plot motif distances relative to motifs from this RBP (--set-rbp-id). Motif plot will be centered on best scoring motif of the RBP for each region. Note that set RBP ID needs to be one of the above selected RBP IDs!"/> + <param name="motif_distance_plot_range" type="integer" value="60" + label="BED score column used for p-value calculations" + help="Set range of motif distance plot. I.e., centered on the set RBP (--set-rbp-id) motifs, motifs within minus and plus --motif-distance-plot-range will be plotted (default: 60)"/> + <param name="motif_min_pair_count" type="integer" value="10" + label="Motif co-occurrence minimum pair count" + help="Minimum count of co-occurrences of a motif with set RBP ID (--set-rbp-id) motif to be reported and plotted (default: 10)"/> + <param name="rbp_min_pair_count" type="integer" value="10" + label="RBP co-occurrence minimum pair count" + help="Minimum amount of co-occurrences of motifs for an RBP ID compared to set RBP ID (--set-rbp-id) motifs to be reported and plotted (default: 10)"/> + + <param name="store_sort_js_in_html" label="Store JS code for table sorting inside HTML?" + type="boolean" checked="False" + help="Store JavaScript code for table sorting inside output HTML files. By default code is stored locally in extra file located in HTML output folder."/> + <param name="plotly_js_source" type="integer" value="1" min="1" max="3" + label="Specify plotly JS code source" + help="1: Store plotly JavaScript code locally inside HTML output folder. 2: Add hyperlink to report HTML file (internet connection required). 3: Store code inside report HTML file (default: 1)"/> + <param name="plotly_plot_code_in_html" label="Store plotly plotting code inside HTML?" + type="boolean" checked="False" + help="Store plotly plotting code inside HTML. By default code is stored in separate HTML files in HTML report output folder."/> + + </section> + + <section name="search_output_options" title="Output options"> + <param name="search_report" label="Output HTML report?" type="boolean" + truevalue="--report" falsevalue="" checked="True" + help="Generate an HTML report containing RBP co-occurrence + combination + distance statistics and plots (default: True)"/> + <param name="search_plot_motifs" label="Plot RBP motifs?" type="boolean" + truevalue="--plot-motifs" falsevalue="" checked="False" + help="Visualize selected RBP motifs, by outputting sequence logos and motif hit statistics into a separate HTML file (default: False)"/> + <param name="sites_bed_fasta_out" label="Output filtered genomic regions BED + FASTA files" type="boolean" + checked="False" + help="Output filtered genomic regions BED/FASTA file used for motif search. Filtered means that the actual regions used for motif search can differ from the input genomic regions, e.g. through default filtering by chromsome ID (only regions with valid IDs), removal of duplicated regions, or through optional extension of the regions"/> + <param name="motif_hits_bed_out" label="Output motif hits BED file" type="boolean" + checked="False" + help="Output motif hits BED file containing motif hits in provided genomic regions for selected RBPs"/> + <param name="contingency_table_out" label="Output contingency table containing co-occurrence p-values" type="boolean" + checked="False" + help="Output contingency table containing co-occurrence p-values (Fisher's exact test) between each RBP pair (see manual for more information)"/> + <param name="region_annotations_out" label="Output genomic region annotations table file?" + type="boolean" checked="False" + help="Output genomic region annotations table file containing assigned annotations for each BED input region. Note that a GTF file has to be provided (default: False)"/> + </section> + </when> + + <!-- rbpbench batch --> + <when value="batch_search_motifs"> + <repeat name="dataset_inputs" min="1" title="Dataset"> + <param name="dataset_bed_file" type="data" format="bed" + label="Genomic regions BED file" + help="Genomic regions (e.g. RBP binding sites) in BED format (>= 6-columns) for RBP binding motif search"/> + <param name="dataset_rbp_id" label="Select RBP for motif search" type="select"> + <options from_data_table='rbp_ids_table' /> + </param> + <param type="text" name="dataset_method_id" value="method_id" + label="Method ID" + help="Method ID which can be used to describe the peak calling method (e.g. clipper_idr). This ID (together with data ID and set RBP ID) defines which search results get compared in RBPBench's comparison mode (see Help below for more details)."/> + <param type="text" name="dataset_data_id" value="data_id" + label="Data ID" + help="Data ID which can be used to describe from which cell type and/or CLIP-seq protocol the data originates (e.g. k562_eclip or pum2_k562_eclip). This ID (together with method ID set RBP ID) defines which search results get compared in RBPBench's comparison mode (see Help below for more details)."/> + </repeat> + + <conditional name="reference_genome"> + <param label="Select reference genome sequence (according to the provided BED files)" name="reference_genome_selector" type="select"> + <option selected="True" value="builtin">Select built-in genome sequence</option> + <option value="history">Select genome sequence from history</option> + </param> + <when value="builtin"> + <param label="Select built-in genome sequence" name="builtin_genome" type="select"> + <options from_data_table="fasta_indexes"> + <filter column="2" type="sort_by" /> + <validator message="No genomes are available for the selected input dataset" type="no_options" /> + </options> + </param> + </when> + <when value="history"> + <param format="fasta" type="data" name="history_genome" label="Select genome sequence in FASTA format from history"/> + </when> + </conditional> + + <section name="search_options" title="Motif search settings"> + <param name="search_ext" type="text" value="0" + label="Up- and downstream extension of genomic regions" + help='Up- and downstream extension of genomic regions in nucleotides (nt). E.g. set to "30" to extend 30 nt on both sides, or "20,10" for different up- and downstream extension (default: 0)'/> + <param name="search_fimo_pval" type="float" value="0.001" + label="FIMO p-value threshold" + help='FIMO p-value threshold (FIMO option: --thresh) for reporting motif hits (default: 0.001)'/> + <param name="search_bed_score_col" type="integer" value="5" + label="BED score column used for p-value calculations" + help="Score column of genomic regions BED files used for p-value calculations. BED score can be e.g. log2 fold change or -log10 p-value of the region (default: 5)"/> + <param name="search_unstranded" label="Treat genomic regions in BED file as NOT strand-specific" type="boolean" + truevalue="--unstranded" falsevalue="" checked="False" + help="Set if genomic regions in BED files are NOT strand-specific, i.e., to look for motifs on both strands of the provided regions. Note that the two strands of a region will still be counted as one region (change with option below) (default: False)"/> + <param name="search_unstranded_ct" label="Count each genomic region twice for RBP hit statistics" type="boolean" + truevalue="--unstranded-ct" falsevalue="" checked="False" + help="Count each genomic region twice for RBP hit statistics when non-strand-specific option above is enabled (default: False)"/> + <param format="txt" type="data" name="fimo_nt_freqs_file" optional="True" + label="Provide FIMO nucleotide frequencies file" + help="Provide FIMO nucleotide frequencies (FIMO option: --bifile) file. By default, an internal frequencies file optimized for human transcripts is used"/> + </section> + + <section name="search_output_options" title="Output options"> + <param name="batch_motif_hits_bed_out" label="Output motif hits BED file" type="boolean" + checked="False" + help="Output motif hits BED file containing motif hits for all input datasets"/> + </section> + + </when> + + <!-- rbpbench batch data collection + table --> + <when value="batch_table_search_motifs"> + + <param name="batch_table_bed_collection" type="data_collection" collection_type="list" format="bed" + label="Data collection containing genomic regions BED files" + help="Data collection containing genomic regions BED files to be processed. Note that dataset names inside collection must correspond to names given in the batch processing table file below"/> + + <param name="batch_table_file" type="data" format="txt,tabular" + label="Provide batch processing table file" + help="Provide batch processing table file with one row for each batch job. Each row contains the tab-delimited information: RBP ID (RBP name), method ID, data ID, dataset name. The dataset name must be present in the supplied data collection of BED files"/> + + <conditional name="reference_genome"> + <param label="Select reference genome sequence (according to the provided BED files)" name="reference_genome_selector" type="select"> + <option selected="True" value="builtin">Select built-in genome sequence</option> + <option value="history">Select genome sequence from history</option> + </param> + <when value="builtin"> + <param label="Select built-in genome sequence" name="builtin_genome" type="select"> + <options from_data_table="fasta_indexes"> + <filter column="2" type="sort_by" /> + <validator message="No genomes are available for the selected input dataset" type="no_options" /> + </options> + </param> + </when> + <when value="history"> + <param format="fasta" type="data" name="history_genome" label="Select genome sequence in FASTA format from history"/> + </when> + </conditional> + + <section name="search_options" title="Motif search settings"> + <param name="search_ext" type="text" value="0" + label="Up- and downstream extension of genomic regions" + help='Up- and downstream extension of genomic regions in nucleotides (nt). E.g. set to "30" to extend 30 nt on both sides, or "20,10" for different up- and downstream extension (default: 0)'/> + <param name="search_fimo_pval" type="float" value="0.001" + label="FIMO p-value threshold" + help='FIMO p-value threshold (FIMO option: --thresh) for reporting motif hits (default: 0.001)'/> + <param name="search_bed_score_col" type="integer" value="5" + label="BED score column used for p-value calculations" + help="Score column of genomic regions BED files used for p-value calculations. BED score can be e.g. log2 fold change or -log10 p-value of the region (default: 5)"/> + <param name="search_unstranded" label="Treat genomic regions in BED file as NOT strand-specific" type="boolean" + truevalue="--unstranded" falsevalue="" checked="False" + help="Set if genomic regions in BED files are NOT strand-specific, i.e., to look for motifs on both strands of the provided regions. Note that the two strands of a region will still be counted as one region (change with option below) (default: False)"/> + <param name="search_unstranded_ct" label="Count each genomic region twice for RBP hit statistics" type="boolean" + truevalue="--unstranded-ct" falsevalue="" checked="False" + help="Count each genomic region twice for RBP hit statistics when non-strand-specific option above is enabled (default: False)"/> + <param format="txt" type="data" name="fimo_nt_freqs_file" optional="True" + label="Provide FIMO nucleotide frequencies file" + help="Provide FIMO nucleotide frequencies (FIMO option: --bifile) file. By default, an internal frequencies file optimized for human transcripts is used"/> + </section> + + <section name="search_output_options" title="Output options"> + <param name="batch_table_motif_hits_bed_out" label="Output motif hits BED file" type="boolean" + checked="False" + help="Output motif hits BED file containing motif hits for all input datasets"/> + </section> + + </when> + + <!-- rbpbench dist --> + <when value="plot_nt_dist"> + + <param name="dist_bed_file" type="data" format="bed" + label="Genomic regions BED file" + help="Genomic regions (e.g. RBP binding sites) in BED format. Zero position for plotting can be defined in options"/> + + <conditional name="reference_genome"> + <param label="Select reference genome sequence (according to BED file)" name="reference_genome_selector" type="select"> + <option selected="True" value="history">Select genome sequence from history</option> + <option value="builtin">Select built-in genome sequence</option> + </param> + <when value="history"> + <param format="fasta" type="data" name="history_genome" label="Select genome sequence in FASTA format from history"/> + </when> + <when value="builtin"> + <param label="Select built-in genome sequence" name="builtin_genome" type="select"> + <options from_data_table="fasta_indexes"> + <filter column="2" type="sort_by" /> + <validator message="No genomes are available for the selected input dataset" type="no_options" /> + </options> + </param> + </when> + </conditional> + + <section name="dist_options" title="Nucleotide distribution plot settings"> + <param name="dist_cp_mode" type="integer" value="1" min="1" max="3" + label="Define zero position for plotting" + help="Define which position of genomic sites to use as zero position for plotting. 1: upstream end position, 2: center position, 3: downstream end position (default: 1)"/> + <param name="dist_ext" type="integer" value="10" + label="Up- and downstream extension of defined genomic positions" + help="Up- and downstream extension of defined genomic positions in nucleotides (nt) to include in plotting (default: 10)"/> + <param name="dist_plot_pdf" label="Plot as PDF?" type="boolean" + truevalue="--plot-pdf" falsevalue="" checked="False" + help="Plot nucleotide distribution as PDF (default: PNG)"/> + <param name="sites_bed_fasta_out" label="Output genomic regions BED + FASTA files" type="boolean" + checked="False" + help="Output genomic regions BED/FASTA file used for plotting"/> + </section> + + </when> + + <!-- rbpbench compare --> + <when value="compare_search_results"> + + <param name="input_tables" type="data" format="tabular" multiple="true" + label="Motif search results" + help="Supply motif search results table files for comparison. These are the hit statistics table files output by single or batch motif search jobs. Both RBP and motif hit statistics table files are needed, and can be from any single or batch search job."/> + + <section name="compare_output_options" title="Output options"> + <param name="compared_motif_hits_table" label="Output compared motif hits table file" type="boolean" + checked="False" + help="Output compared motif hits table file showing motif hits and which data or method IDs contain them"/> + <param name="compared_motif_hits_bed" label="Output compared motif hits BED file" type="boolean" + checked="False" + help="Output compared motif hits table file showing motif hits and which data or method IDs contain them in BED format"/> + <param name="comparisons_stats_out" label="Output comparison statistics table file" type="boolean" + checked="False" + help="Output comparison statistics table file containing the statistics found in the comparison HTML report"/> + <param name="store_sort_js_in_html" label="Store JS code for table sorting inside HTML?" + type="boolean" checked="False" + help="Store JavaScript code for table sorting inside output HTML files. By default code is stored locally in extra file located in HTML output folder."/> + </section> + </when> + + </conditional> + + </inputs> + + <outputs> + + <!-- rbpbench search outputs --> + <data name="rbp_hit_stats_file" format="tabular" from_work_dir="rbp_hit_stats.tsv" label="${tool.name} on ${on_string}: RBP hit statistics table file"> + <filter>action_type["action_type_selector"] == "search_motifs"</filter> + </data> + <data name="motif_hit_stats_file" format="tabular" from_work_dir="motif_hit_stats.tsv" label="${tool.name} on ${on_string}: Motif hit statistics table file"> + <filter>action_type["action_type_selector"] == "search_motifs"</filter> + </data> + <data name="search_report_html_file" format="html" from_work_dir="report.rbpbench_search.html" label="${tool.name} on ${on_string}: Search report HTML file"> + <filter>action_type["action_type_selector"] == "search_motifs" and action_type["search_output_options"]["search_report"]</filter> + </data> + <data name="motif_plots_html_file" format="html" from_work_dir="motif_plots.rbpbench_search.html" label="${tool.name} on ${on_string}: Motif plots HTML file"> + <filter>action_type["action_type_selector"] == "search_motifs" and action_type["search_output_options"]["search_plot_motifs"]</filter> + </data> + <data name="in_sites_bed_file" format="bed" from_work_dir="in_sites.filtered.bed" label="${tool.name} on ${on_string}: Genomic regions used for motif search BED file"> + <filter>action_type["action_type_selector"] == "search_motifs" and action_type["search_output_options"]["sites_bed_fasta_out"]</filter> + </data> + <data name="in_sites_fa_file" format="fasta" from_work_dir="in_sites.filtered.fa" label="${tool.name} on ${on_string}: Genomic regions used for motif search FASTA file"> + <filter>action_type["action_type_selector"] == "search_motifs" and action_type["search_output_options"]["sites_bed_fasta_out"]</filter> + </data> + <data name="motif_hits_bed_file" format="bed" from_work_dir="motif_hits.rbpbench_search.bed" label="${tool.name} on ${on_string}: Motif hits on genomic regions BED file"> + <filter>action_type["action_type_selector"] == "search_motifs" and action_type["search_output_options"]["motif_hits_bed_out"]</filter> + </data> + <data name="contingency_table_file" format="tabular" from_work_dir="contingency_table_results.tsv" label="${tool.name} on ${on_string}: RBP co-occurrence contingency table file"> + <filter>action_type["action_type_selector"] == "search_motifs" and action_type["search_output_options"]["contingency_table_out"]</filter> + </data> + <data name="region_annotations_file" format="tabular" from_work_dir="region_annotations.tsv" label="${tool.name} on ${on_string}: genomic region annotations table file"> + <filter>action_type["action_type_selector"] == "search_motifs" and action_type["search_output_options"]["region_annotations_out"] and action_type["report_plotting_options"]["gtf_file"]</filter> + </data> + + <!-- rbpbench batch outputs --> + <data name="batch_rbp_hit_stats_file" format="tabular" from_work_dir="rbp_hit_stats.tsv" label="${tool.name} on ${on_string}: Batch RBP hit statistics table file"> + <filter>action_type["action_type_selector"] == "batch_search_motifs"</filter> + </data> + <data name="batch_motif_hit_stats_file" format="tabular" from_work_dir="motif_hit_stats.tsv" label="${tool.name} on ${on_string}: Batch motif hit statistics table file"> + <filter>action_type["action_type_selector"] == "batch_search_motifs"</filter> + </data> + <data name="batch_motif_hits_bed_file" format="bed" from_work_dir="motif_hits.rbpbench_batch.bed" label="${tool.name} on ${on_string}: Batch motif hits on genomic regions BED files"> + <filter>action_type["action_type_selector"] == "batch_search_motifs" and action_type["search_output_options"]["batch_motif_hits_bed_out"]</filter> + </data> + + <!-- rbpbench batch table outputs --> + <data name="batch_table_rbp_hit_stats_file" format="tabular" from_work_dir="rbp_hit_stats.tsv" label="${tool.name} on ${on_string}: Batch data collection RBP hit statistics table file"> + <filter>action_type["action_type_selector"] == "batch_table_search_motifs"</filter> + </data> + <data name="batch_table_motif_hit_stats_file" format="tabular" from_work_dir="motif_hit_stats.tsv" label="${tool.name} on ${on_string}: Batch data collection motif hit statistics table file"> + <filter>action_type["action_type_selector"] == "batch_table_search_motifs"</filter> + </data> + <data name="batch_table_motif_hits_bed_file" format="bed" from_work_dir="motif_hits.rbpbench_batch.bed" label="${tool.name} on ${on_string}: Motif hits on genomic regions BED files from data collection"> + <filter>action_type["action_type_selector"] == "batch_table_search_motifs" and action_type["search_output_options"]["batch_table_motif_hits_bed_out"]</filter> + </data> + + <!-- rbpbench dist outputs --> + <data name="nt_dist_plot_png_file" format="png" from_work_dir="nt_dist_zero_pos.png" label="${tool.name} on ${on_string}: Nucleotide distribution plot PNG file"> + <filter>action_type["action_type_selector"] == "plot_nt_dist" and not action_type["dist_options"]["dist_plot_pdf"]</filter> + </data> + <data name="nt_dist_plot_pdf_file" format="pdf" from_work_dir="nt_dist_zero_pos.pdf" label="${tool.name} on ${on_string}: Nucleotide distribution plot PDF file"> + <filter>action_type["action_type_selector"] == "plot_nt_dist" and action_type["dist_options"]["dist_plot_pdf"]</filter> + </data> + <data name="plot_sites_bed_file" format="bed" from_work_dir="in_sites.filtered.bed" label="${tool.name} on ${on_string}: Genomic regions used for plotting BED file"> + <filter>action_type["action_type_selector"] == "plot_nt_dist" and action_type["dist_options"]["sites_bed_fasta_out"]</filter> + </data> + <data name="plot_sites_fa_file" format="fasta" from_work_dir="in_sites.filtered.fa" label="${tool.name} on ${on_string}: Genomic regions used for plotting FASTA file"> + <filter>action_type["action_type_selector"] == "plot_nt_dist" and action_type["dist_options"]["sites_bed_fasta_out"]</filter> + </data> + + <!-- rbpbench compare outputs --> + <data name="compare_report_html_file" format="html" from_work_dir="report.rbpbench_compare.html" label="${tool.name} on ${on_string}: Comparison report HTML file"> + <filter>action_type["action_type_selector"] == "compare_search_results"</filter> + </data> + <data name="compared_motif_hits_bed_file" format="bed" from_work_dir="motif_hits.rbpbench_compare.bed" label="${tool.name} on ${on_string}: Compared motif hits BED file"> + <filter>action_type["action_type_selector"] == "compare_search_results" and action_type["compare_search_results"]["compared_motif_hits_bed"]</filter> + </data> + <data name="compared_motif_hits_table_file" format="tabular" from_work_dir="motif_hits.rbpbench_compare.tsv" label="${tool.name} on ${on_string}: Compared motif hits table file"> + <filter>action_type["action_type_selector"] == "compare_search_results" and action_type["compare_search_results"]["compared_motif_hits_table"]</filter> + </data> + <data name="compared_stats_table_file" format="tabular" from_work_dir="comparison_stats.rbpbench_compare.tsv" label="${tool.name} on ${on_string}: Comparison statistics table file"> + <filter>action_type["action_type_selector"] == "compare_search_results" and action_type["compare_search_results"]["comparisons_stats_out"]</filter> + </data> + + </outputs> + + <tests> + + <!-- rbpbench search tests --> + <test expect_num_outputs="7"> + <param name="action_type_selector" value="search_motifs"/> + <param name="reference_genome_selector" value="history" /> + <param name="history_genome" value="test.fa" /> + <param name="search_bed_file" value="test.bed" ftype="bed"/> + <param name="select_rbps_selector" value="list_db_rbps"/> + <param name="database" value="PUM1,PUM2" /> + <param name="search_report" value="True"/> + <param name="search_plot_motifs" value="False"/> + <param name="sites_bed_fasta_out" value="True"/> + <param name="motif_hits_bed_out" value="True"/> + <param name="contingency_table_out" value="True"/> + <output name="rbp_hit_stats_file" file="rbp_hit_stats.rbpbench_search.tsv" compare="sim_size"/> + <output name="motif_hit_stats_file" file="motif_hit_stats.rbpbench_search.tsv" compare="sim_size"/> + <output name="search_report_html_file" file="report.rbpbench_search.html" compare="sim_size"/> + <output name="in_sites_bed_file" file="in_sites.filtered.rbpbench_search.bed"/> + <output name="in_sites_fa_file" file="in_sites.filtered.rbpbench_search.fa"/> + <output name="motif_hits_bed_file" file="motif_hits.rbpbench_search.bed"/> + <output name="contingency_table_file" file="contingency_table_results.rbpbench_search.tsv"/> + </test> + <!-- test builtin fasta --> + <test expect_num_outputs="7"> + <param name="action_type_selector" value="search_motifs"/> + <param name="reference_genome_selector" value="builtin" /> + <param name="builtin_genome" value="testid" /> + <param name="search_bed_file" value="test.bed" ftype="bed"/> + <param name="select_rbps_selector" value="list_db_rbps"/> + <param name="database" value="PUM1,PUM2" /> + <param name="search_report" value="True"/> + <param name="search_plot_motifs" value="False"/> + <param name="sites_bed_fasta_out" value="True"/> + <param name="motif_hits_bed_out" value="True"/> + <param name="contingency_table_out" value="True"/> + <output name="rbp_hit_stats_file" file="rbp_hit_stats.rbpbench_search.tsv" compare="sim_size"/> + <output name="motif_hit_stats_file" file="motif_hit_stats.rbpbench_search.tsv" compare="sim_size"/> + <output name="search_report_html_file" file="report.rbpbench_search.html" compare="sim_size"/> + <output name="in_sites_bed_file" file="in_sites.filtered.rbpbench_search.bed"/> + <output name="in_sites_fa_file" file="in_sites.filtered.rbpbench_search.fa"/> + <output name="motif_hits_bed_file" file="motif_hits.rbpbench_search.bed"/> + <output name="contingency_table_file" file="contingency_table_results.rbpbench_search.tsv"/> + </test> + + <test expect_num_outputs="2"> + <param name="action_type_selector" value="search_motifs"/> + <param name="reference_genome_selector" value="history" /> + <param name="history_genome" value="test.slbp_user.fa" /> + <param name="search_bed_file" value="test.slbp_user.bed" ftype="bed"/> + <param name="user_rbp_selector" value="structure"/> + <param name="cm_model_file" value="SLBP_USER.cm" /> + <param name="str_rbp_id" value="SLBP_USER" /> + <param name="search_report" value="False"/> + <output name="rbp_hit_stats_file" file="rbp_hit_stats.rbpbench_search.slbp_user.tsv" compare="sim_size"/> + <output name="motif_hit_stats_file" file="motif_hit_stats.rbpbench_search.slbp_user.tsv" compare="sim_size"/> + </test> + <test expect_num_outputs="3"> + <param name="action_type_selector" value="search_motifs"/> + <param name="reference_genome_selector" value="history" /> + <param name="history_genome" value="test.fa" /> + <param name="search_bed_file" value="test.bed" ftype="bed"/> + <param name="select_db_selector" value="default_db"/> + <param name="select_rbps_selector" value="all_db_rbps"/> + <param name="search_report" value="False"/> + <param name="search_plot_motifs" value="False"/> + <param name="sites_bed_fasta_out" value="False"/> + <param name="motif_hits_bed_out" value="True"/> + <param name="contingency_table_out" value="False"/> + <output name="motif_hits_bed_file" file="motif_hits.rbpbench_search.test_all.bed"/> + </test> + <test expect_num_outputs="4"> + <param name="action_type_selector" value="search_motifs"/> + <param name="reference_genome_selector" value="history" /> + <param name="history_genome" value="test.fa" /> + <param name="search_bed_file" value="test.bed" ftype="bed"/> + <param name="gtf_file" value="test_search.gtf" ftype="gtf"/> + <param name="select_db_selector" value="default_db"/> + <param name="select_rbps_selector" value="all_db_rbps"/> + <param name="search_report" value="True"/> + <param name="search_plot_motifs" value="False"/> + <param name="sites_bed_fasta_out" value="False"/> + <param name="motif_hits_bed_out" value="False"/> + <param name="contingency_table_out" value="False"/> + <param name="region_annotations_out" value="True"/> + <output name="region_annotations_file" file="test_search_gtf.region_annotations.tsv"/> + </test> + <test expect_num_outputs="3"> + <param name="action_type_selector" value="search_motifs"/> + <param name="reference_genome_selector" value="history" /> + <param name="history_genome" value="test.fa" /> + <param name="search_bed_file" value="test.bed" ftype="bed"/> + <param name="select_db_selector" value="custom_db"/> + <param name="custom_db_id" value="custom_yo" /> + <param name="custom_db_info_file" value="test_custom.info.txt" /> + <param name="custom_db_meme_xml_file" value="test_custom.seq_motifs.meme" /> + <param name="custom_db_cm_model_file" value="test_custom.str_motifs.cm" /> + <param name="custom_db_rbp_ids_list" value="PUM1 PUM2 SLBP" /> + <param name="search_report" value="False"/> + <param name="search_plot_motifs" value="False"/> + <param name="sites_bed_fasta_out" value="False"/> + <param name="motif_hits_bed_out" value="True"/> + <param name="contingency_table_out" value="False"/> + <param name="region_annotations_out" value="False"/> + <output name="motif_hits_bed_file" file="test_custom.motif_hits.rbpbench_search.bed"/> + </test> + + <!-- rbpbench batch tests --> + <test expect_num_outputs="3"> + <param name="action_type_selector" value="batch_search_motifs"/> + <param name="reference_genome_selector" value="history" /> + <param name="history_genome" value="test.fa" /> + <repeat name="dataset_inputs"> + <param name="dataset_bed_file" value="test.bed"/> + <param name="dataset_method_id" value="method-id1" /> + <param name="dataset_data_id" value="data-id1" /> + <param name="dataset_rbp_id" value="PUM1" /> + </repeat> + <repeat name="dataset_inputs"> + <param name="dataset_bed_file" value="test.bed"/> + <param name="dataset_method_id" value="method-id2" /> + <param name="dataset_data_id" value="data-id2" /> + <param name="dataset_rbp_id" value="PUM2" /> + </repeat> + <param name="batch_motif_hits_bed_out" value="True"/> + <output name="batch_rbp_hit_stats_file" file="rbp_hit_stats.test_batch.tsv" compare="sim_size"/> + <output name="batch_motif_hit_stats_file" file="motif_hit_stats.test_batch.tsv" compare="sim_size"/> + <output name="batch_motif_hits_bed_file" file="motif_hits.rbpbench_batch.test_batch.bed"/> + </test> + + <!-- rbpbench batch table tests --> + <test expect_num_outputs="3"> + <param name="action_type_selector" value="batch_table_search_motifs"/> + <param name="reference_genome_selector" value="history" /> + <param name="history_genome" value="test.fa" /> + <param name="batch_table_bed_collection"> + <collection type="list"> + <element name="test1.bed" value="test1.bed"/> + <element name="test2.bed" value="test2.bed"/> + </collection> + </param> + <param name="batch_table_file" value="test_table.txt"/> + <param name="batch_table_motif_hits_bed_out" value="True"/> + <output name="batch_table_rbp_hit_stats_file" file="rbp_hit_stats.table_test.tsv" compare="sim_size"/> + <output name="batch_table_motif_hit_stats_file" file="motif_hit_stats.table_test.tsv" compare="sim_size"/> + <output name="batch_table_motif_hits_bed_file" file="motif_hits.rbpbench_batch.table_test.bed"/> + </test> + + <!-- rbpbench compare tests --> + <test expect_num_outputs="4"> + <param name="action_type_selector" value="compare_search_results"/> + <param name="input_tables" value="rbp_hit_stats.compare_test.dewseq.tsv,rbp_hit_stats.compare_test.clipper_idr.tsv,motif_hit_stats.compare_test.dewseq.tsv,motif_hit_stats.compare_test.clipper_idr.tsv" ftype="tabular" /> + <param name="compared_motif_hits_table" value="True"/> + <param name="compared_motif_hits_bed" value="True"/> + <param name="comparisons_stats_out" value="True"/> + <output name="compare_report_html_file" file="report.rbpbench_compare.test.html" compare="sim_size"/> + <output name="compared_motif_hits_bed_file" file="motif_hits.rbpbench_compare.test.bed"/> + <output name="compared_motif_hits_table_file" file="motif_hits.rbpbench_compare.test.tsv"/> + <output name="compared_stats_table_file" file="comparison_stats.rbpbench_compare.test.tsv"/> + </test> + + </tests> + <help><![CDATA[ + + +**What is RBPBench?** + + +RBPBench_ is multi-function tool to evaluate CLIP-seq and other genomic region +data using a comprehensive collection of known RNA-binding protein (RBP) binding motifs. +RBPBench can be used for a variety of purposes, from RBP motif search (database or +user-supplied RBPs) in genomic regions, over motif co-occurrence analysis, to benchmarking +CLIP-seq peak caller methods as well as comparisons across cell types and +CLIP-seq protocols. + +----- + +**RBPBench program modes** + +RBPBench on Galaxy provides the following main functions (Choose on top via "Select RBPBench program mode"): + +1) Search RBP binding motifs in genomic regions +2) Search RBP binding motifs in genomic regions (multiple inputs) +3) Search RBP binding motifs in genomic regions (data collection input) +4) Plot nucleotide distribution at genomic positions +5) Compare different search results + + +**1. Search RBP binding motifs in genomic regions** + +In this mode we can select any number of RBPs of interest and search for RBP binding motifs in a given +set of genomic regions (*Genomic regions BED file*). A built-in high-quality database of human RBP binding motifs +(currently containing 259 RBPs and 605 motifs) is used by default. Moreover, users can add own motifs +(*Add user-supplied motifs*), as well as defining their own database (*Provide a custom RBP motif database*). +Both sequence (MEME/DREME XML format) and structure motifs (covariance models) are supported. +Comprehensive hit statistics (both on RBP and single motif level) are output as table files, +together with an informative HTML report containing various plots and tables +(see Output options to control what files are output). +Hit statistics output table formats are described in the RBPBench documentation_. +The HTML report includes statistics for each RBP on enrichment of motifs in higher scoring regions, +as well as a heatmap of RBP co-occurrences in genomic regions, and an upset plot +on present RBP combinations (*HTML report options* for finetuning). +If a GTF file is provided (*HTML report options -> GTF file*), genomic region annotations are also added to the regions and plots. +Furthermore, motif distances (RBP and motif level) can be plotted relative to a set reference RBP +(*HTML report options -> Set reference RBP ID*). +Motif search settings can be adapted, e.g. to apply up- and/or downstream extension to the genomic regions +before search. Motifs for selected RBPs can also be plotted in a separate HTML file (*Output options -> Plot RBP motifs*). +To compare motif search results (mode: *Compare different search results*), +data ID and method ID can be set accordingly (more details in sections 2, 3, and 5). + + +**2. Search RBP binding motifs in genomic regions (multiple inputs)** + +This mode allows the input of more than one set of genomic regions (via *+ Insert Dataset*). +For each input, an RBP for motif search needs to be selected. Optionally (for comparing +different search results), descriptive data + method IDs can be added (also see *Compare different search results*). +For example, if two different peak calling methods (method1, method2) have been used to +extract RBP binding regions from CLIP-seq data of RBP RBPX, and we want to compare these two methods later on, we would: +*+ Insert Dataset*: input the set (i.e., BED file) produced by method1, choose the CLIP-ped RBP (RBPX) + add method ID "method1". +*+ Insert Dataset*: input the set produced by method2, again choose RBPX, and add method ID "method2". +The data ID we keep constant, ideally choosing an ID that describes the data (e.g. cell type, CLIP-seq protocol, CLIP-ped RBP). +For example, if the cell type is K562, and the CLIP-seq protocol is eCLIP, we could specify +the data ID "K562_eCLIP" or "RBPX_K562_eCLIP". We can repeat this for other proteins by +adding the respective inputs. Finally, for comparing the two methods, +all we need to do is to use the two produced hit statistics output tables (RBP + motif hit statistics) +as inputs in *Compare different search results* mode. +The same also works the other way around, by keeping the method ID constant and changing the data ID. +For example, if we want to compare motif search results across different cell types, we can use +different data IDs while keeping the method ID. + + +**3. Search RBP binding motifs in genomic regions (data collection input)** + +This mode is identical to the previous one (multiple inputs), except that instead of +manually defining each input (dataset, RBP, method ID, data ID), we simply +input a table containing all the information, as well as a dataset collection containing the datasets. +It is thus the preferable mode if we want to compare a large number of datasets +(concept of comparing sets via method ID and data ID described in the previous section). +The input table (batch processing table file) has the following format +(tab-separated columns: RBP ID, method ID, data ID, BED genomic regions file name): + +========== ============ =============== ============================= +PUM1 method1 K562_eCLIP PUM1.K562_eclip.method1.bed +PUM1 method2 K562_eCLIP PUM1.K562_eclip.method2.bed +PUM1 method3 K562_eCLIP PUM1.K562_eclip.method3.bed +PUM2 method1 K562_eCLIP PUM2.K562_eclip.method1.bed +PUM2 method2 K562_eCLIP PUM2.K562_eclip.method2.bed +PUM2 method3 K562_eCLIP PUM2.K562_eclip.method3.bed +SLBP method1 K562_eCLIP SLBP.K562_eclip.method1.bed +SLBP method2 K562_eCLIP SLBP.K562_eclip.method2.bed +SLBP method3 K562_eCLIP SLBP.K562_eclip.method3.bed +========== ============ =============== ============================= + +NOTE that the table file name needs to correspond to the name of the dataset inside the +dataset collection. Conveniently, if you upload files to Galaxy and make a dataset collection out of them, +the dataset names will correspond to the uploaded file names. +In the above table, we would produce search results for three different +methods, on three different RBPs. +Likewise, if we would want to compare motif search results across cell types, +the table could look like this: + +========== ============ =============== ============================= +PUM1 method1 K562_eCLIP PUM1.K562_eclip.method1.bed +PUM1 method1 HepG2_eCLIP PUM1.HepG2_eclip.method1.bed +PUM2 method1 K562_eCLIP PUM2.K562_eclip.method1.bed +PUM2 method1 HepG2_eCLIP PUM2.HepG2_eclip.method1.bed +SLBP method1 K562_eCLIP SLBP.K562_eclip.method1.bed +SLBP method1 HepG2_eCLIP SLBP.HepG2_eclip.method1.bed +========== ============ =============== ============================= + +Here we would create motif search results across cell types K562 and HepG2, while keeping the peak calling +method ID constant ("method1"). +As with the two already discussed search modes, +the resulting hit statistics output table files (RBP + motif hit statistics) +can subsequently serve as inputs to RBPBench's comparison mode (*Compare different search results*, section 5). + + +**4. Plot nucleotide distribution at genomic positions** + +In this mode, a set of genomic regions is input and the nucleotide distribution is plotted +around a defined center positions (*Nucleotide distribution plot settings -> Define zero position for plotting*). By default, +the upstream end position of each region is used (other choices are center and downstream end). +This for example enables us to look at CLIP-seq crosslink positions and potential nucleotide biases at these sites. + + +**5. Compare different search results** + +This mode is used to compare different motif search results (produced by any of the three motif search modes +described above). Inputs are the RBP and motif hit statistics table files output by the motif search modes. +As exemplified in the previous sections, the set method IDs and +data IDs (together with the selected RBP IDs) define what gets compared in comparison mode. +Based on the IDs in the input tables, RBPBench looks for combinations of RBP ID+method ID+data ID, and produces +method-ID-centered (with fixed RBP ID + data ID) and / or data-ID-centered (with fixed RBP ID + method ID) comparisons. +At least two different IDs are needed for a comparison (e.g. two different method IDs or two different data IDs, with same RBP ID). +The comparison results are presented in an HTML report file, containing a hit statistics table and a +Venn diagram plot for each found combination. Moreover, the report results are output as table files, +and the combined motifs are output in BED format, for a data ID / method ID centered comparison e.g. inside a Genome Viewer. +Comparing numbers of unique and shared motif hits between methods also serves as a way of benchmarking different methods. +Since no ground truth (i.e., set of true / experimentally verified transcriptome-wide binding sites of an RBP) exists, one obvious way to +benchmark peak calling methods is to look at the enrichment of known RBP binding motifs in regions reported by the peak callers. +RBPBench makes such evaluations easy, especially by combining modes 2,3, and 5. + + +----- + +**Tool documentation & repository** + +For more information (including a webserver tutorial) please visit the RBPBench website: + +https://backofenlab.github.io/RBPBench + + +The RBPBench repository can be found at: + +https://github.com/michauhl/RBPBench + +The GitHub repository hosts the command line version of RBPBench and also includes a +comprehensive manual with installation instructions and various usage examples. + + +.. _RBPBench: https://github.com/michauhl/RBPBench +.. _documentation: https://github.com/michauhl/RBPBench#hit-statistics-table-files + + ]]></help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SLBP_USER.cm Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,385 @@ +INFERNAL1/a [1.1.3 | Nov 2019] +NAME Histone3 +ACC RF00032 +DESC Histone 3' UTR stem-loop +STATES 142 +NODES 42 +CLEN 46 +W 57 +ALPH RNA +RF no +CONS yes +MAP yes +DATE Fri Apr 4 13:03:46 2014 +COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED +COM [2] /nfs/production/xfam/rfam/software/bin/cmcalibrate --mpi CM +PBEGIN 0.05 +PEND 0.05 +WBETA 1e-07 +QDBBETA1 1e-07 +QDBBETA2 1e-15 +N2OMEGA 1.52588e-05 +N3OMEGA 1.52588e-05 +ELSELF -0.08926734 +NSEQ 46 +EFFN 46.000000 +CKSUM 471917655 +NULL 0.000 0.000 0.000 0.000 +GA 25.00 +TC 25.00 +NC 24.90 +EFP7GF -8.9961 0.74543 +ECMLC 0.73248 -4.63583 3.49505 1600000 463131 0.002591 +ECMGC 0.50982 -9.05666 1.92502 1600000 108029 0.003703 +ECMLI 0.86412 -1.32523 4.80439 1600000 239617 0.005008 +ECMGI 0.55516 -6.80684 2.91667 1600000 88393 0.004525 +CM + [ ROOT 0 ] - - - - - - + S 0 -1 0 1 4 1 1 57 76 -10.705 -10.912 -0.004 -9.326 + IL 1 1 2 1 4 1 19 64 83 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 + IR 2 2 3 2 3 1 19 63 81 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 1 ] 1 - c - - - + ML 3 2 3 5 3 1 19 57 76 -11.622 -0.002 -10.276 0.274 0.676 -1.683 -0.183 + D 4 2 3 5 3 0 15 58 76 -6.174 -1.687 -0.566 + IL 5 5 3 5 3 1 18 62 80 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 2 ] 2 - c - - - + ML 6 5 3 8 3 1 18 56 75 -11.622 -0.002 -10.276 0.562 0.685 -1.974 -0.595 + D 7 5 3 8 3 0 15 57 75 -6.174 -1.687 -0.566 + IL 8 8 3 8 3 1 17 61 79 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 3 ] 3 - A - - - + ML 9 8 3 11 3 1 17 55 74 -11.622 -0.002 -10.276 1.588 -1.105 -4.684 -1.031 + D 10 8 3 11 3 0 14 56 74 -6.174 -1.687 -0.566 + IL 11 11 3 11 3 1 17 60 78 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 4 ] 4 - A - - - + ML 12 11 3 14 3 1 16 54 73 -11.622 -0.002 -10.276 1.035 -0.025 -1.895 -0.517 + D 13 11 3 14 3 0 14 55 73 -6.174 -1.687 -0.566 + IL 14 14 3 14 3 1 16 59 77 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 5 ] 5 - a - - - + ML 15 14 3 17 3 1 15 53 72 -11.923 -0.687 -1.402 0.970 0.662 -4.530 -1.266 + D 16 14 3 17 3 0 14 52 71 -5.620 -0.734 -1.403 + IL 17 17 3 17 3 1 15 55 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 6 ] - 47 - U - - + MR 18 17 3 20 3 1 14 52 71 -11.239 -0.003 -9.556 -1.280 -3.255 -0.399 1.446 + D 19 17 3 20 3 0 13 51 70 -11.650 -0.025 -5.880 + IR 20 20 3 20 3 1 12 54 72 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 7 ] - 46 - g - - + MR 21 20 3 23 3 1 14 51 70 -11.923 -0.002 -10.241 0.333 -0.456 0.341 -0.425 + D 22 20 3 23 3 0 8 50 68 -6.390 -1.568 -0.620 + IR 23 23 3 23 3 1 12 53 71 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 8 ] - 45 - U - - + MR 24 23 3 26 3 1 13 50 69 -11.923 -0.002 -10.241 0.022 -0.397 -2.351 1.021 + D 25 23 3 26 3 0 7 49 67 -6.390 -1.568 -0.620 + IR 26 26 3 26 3 1 11 52 70 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 9 ] - 44 - u - - + MR 27 26 3 29 3 1 12 49 68 -11.923 -0.002 -10.241 0.188 -0.473 -0.169 0.323 + D 28 26 3 29 3 0 6 48 66 -6.390 -1.568 -0.620 + IR 29 29 3 29 3 1 10 51 69 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 10 ] - 43 - u - - + MR 30 29 3 32 3 1 11 48 67 -11.923 -0.002 -10.241 0.043 -1.204 0.229 0.448 + D 31 29 3 32 3 0 5 47 65 -6.390 -1.568 -0.620 + IR 32 32 3 32 3 1 10 50 68 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 11 ] - 42 - u - - + MR 33 32 3 35 3 1 10 47 66 -11.923 -0.037 -5.328 0.283 -0.639 -0.668 0.596 + D 34 32 3 35 3 0 5 46 64 -6.390 -1.568 -0.620 + IR 35 35 3 35 3 1 9 49 67 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 12 ] - 41 - a - - + MR 36 35 3 38 3 1 9 46 65 -11.888 -0.002 -10.205 0.690 -2.247 0.302 -0.084 + D 37 35 3 38 3 0 4 45 64 -8.147 -0.315 -2.376 + IR 38 38 3 38 3 1 7 48 66 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 13 ] - 40 - a - - + MR 39 38 3 41 3 1 8 45 64 -11.923 -0.002 -10.241 0.896 -0.277 -0.185 -1.204 + D 40 38 3 41 3 0 2 44 62 -6.390 -1.568 -0.620 + IR 41 41 3 41 3 1 6 47 65 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 14 ] - 39 - A - - + MR 42 41 3 44 3 1 7 44 63 -11.923 -0.002 -10.241 1.147 -1.015 -0.320 -1.029 + D 43 41 3 44 3 0 1 43 61 -6.390 -1.568 -0.620 + IR 44 44 3 44 3 1 5 46 64 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 15 ] - 38 - a - - + MR 45 44 3 47 3 1 7 43 62 -11.923 -0.027 -5.794 0.871 -0.426 -0.479 -0.497 + D 46 44 3 47 3 0 1 42 60 -6.390 -1.568 -0.620 + IR 47 47 3 47 3 1 5 45 63 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 16 ] - 37 - a - - + MR 48 47 3 50 3 1 6 42 61 -11.898 -0.002 -10.216 0.726 -0.863 -0.477 0.109 + D 49 47 3 50 3 0 0 41 60 -7.823 -0.406 -2.053 + IR 50 50 3 50 3 1 3 44 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 17 ] - 36 - a - - + MR 51 50 3 53 3 1 5 41 60 -11.923 -0.002 -10.241 0.725 -1.911 -0.230 0.297 + D 52 50 3 53 3 0 0 40 58 -6.390 -1.568 -0.620 + IR 53 53 3 53 3 1 3 43 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 18 ] - 35 - a - - + MR 54 53 3 56 3 1 4 40 59 -11.923 -0.002 -10.241 0.828 -0.827 -1.719 0.441 + D 55 53 3 56 3 0 0 39 57 -6.390 -1.568 -0.620 + IR 56 56 3 56 3 1 2 42 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 19 ] - 34 - c - - + MR 57 56 3 59 3 1 3 39 58 -11.923 -0.002 -10.241 0.119 0.695 -0.517 -0.745 + D 58 56 3 59 3 0 0 38 56 -6.390 -1.568 -0.620 + IR 59 59 3 59 3 1 2 41 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 20 ] - 33 - a - - + MR 60 59 3 62 3 1 2 38 57 -11.923 -0.002 -10.241 0.569 -0.255 -1.396 0.378 + D 61 59 3 62 3 0 0 37 55 -6.390 -1.568 -0.620 + IR 62 62 3 62 3 1 1 40 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 21 ] - 32 - u - - + MR 63 62 3 65 3 1 1 37 56 -11.923 -0.056 -4.714 0.347 -0.205 -0.853 0.387 + D 64 62 3 65 3 0 0 36 54 -6.390 -1.568 -0.620 + IR 65 65 3 65 3 1 1 39 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 22 ] - 31 - u - - + MR 66 65 3 68 3 1 3 36 55 -11.868 -0.002 -10.186 0.706 -1.486 -1.611 0.752 + D 67 65 3 68 3 0 0 35 54 -8.618 -0.220 -2.847 + IR 68 68 3 68 3 1 1 38 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 23 ] - 30 - u - - + MR 69 68 3 71 3 1 2 35 54 -11.923 -0.002 -10.241 -0.972 -0.369 0.214 0.638 + D 70 68 3 71 3 0 0 34 52 -6.390 -1.568 -0.620 + IR 71 71 3 71 3 1 1 37 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 24 ] - 29 - A - - + MR 72 71 3 74 3 1 1 34 53 -11.923 -0.047 -4.982 1.166 -1.748 -1.275 0.063 + D 73 71 3 74 3 0 0 33 52 -6.390 -1.568 -0.620 + IR 74 74 3 74 3 1 1 36 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 25 ] - 28 - c - - + MR 75 74 3 77 3 1 1 33 52 -11.878 -0.002 -10.195 -0.910 0.584 -0.997 0.554 + D 76 74 3 77 3 0 0 32 51 -8.406 -0.258 -2.636 + IR 77 77 3 77 3 1 1 35 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 26 ] - 27 - A - - + MR 78 77 3 80 3 1 1 32 51 -11.923 -0.071 -4.384 1.458 -1.557 -2.019 -0.586 + D 79 77 3 80 3 0 0 31 50 -6.390 -1.568 -0.620 + IR 80 80 3 80 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 27 ] - 26 - a - - + MR 81 80 3 83 3 1 1 31 50 -1.344 -0.725 -10.171 0.698 0.567 -2.058 -0.607 + D 82 80 3 83 3 0 0 31 49 -0.277 -4.066 -3.118 + IR 83 83 3 83 3 1 1 31 49 -6.042 -0.027 -8.281 0.000 0.000 0.000 0.000 + [ MATR 28 ] - 24 - c - - + MR 84 83 3 86 3 1 1 30 48 -11.923 -0.002 -10.241 0.331 0.903 -2.658 -0.486 + D 85 83 3 86 3 0 0 29 47 -6.390 -1.568 -0.620 + IR 86 86 3 86 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 29 ] - 23 - C - - + MR 87 86 3 89 3 1 1 29 47 -11.923 -0.002 -10.241 -2.740 1.578 -5.132 -0.259 + D 88 86 3 89 3 0 0 28 46 -6.390 -1.568 -0.620 + IR 89 89 3 89 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 30 ] - 22 - A - - + MR 90 89 3 92 5 1 1 28 46 -10.571 -0.003 -10.387 -10.599 -11.491 1.957 -3.517 -6.202 -6.036 + D 91 89 3 92 5 0 0 27 45 -5.352 -0.707 -2.978 -4.409 -2.404 + IR 92 92 3 92 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 31 ] 6 21 G C - - + MP 93 92 3 97 6 2 2 27 45 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -9.446 -6.202 -11.294 -3.624 -11.134 -7.406 -5.494 -10.940 -7.562 3.944 -7.769 -1.149 -5.842 -7.856 -7.917 -10.190 + ML 94 92 3 97 6 1 1 26 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 95 92 3 97 6 1 1 25 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 96 92 3 97 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 97 97 5 97 6 1 1 27 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 98 98 6 98 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 32 ] 7 20 G C - - + MP 99 98 6 103 6 2 2 25 43 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -9.520 -6.204 -11.599 -3.658 -11.128 -7.383 -5.483 -11.144 -7.569 3.980 -7.767 -4.127 -5.848 -7.844 -7.915 -10.583 + ML 100 98 6 103 6 1 1 24 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 101 98 6 103 6 1 1 24 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 102 98 6 103 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 103 103 5 103 6 1 1 25 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 104 104 6 104 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 33 ] 8 19 C G - - + MP 105 104 6 109 6 2 2 23 41 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -8.195 -8.273 -7.664 0.485 -6.102 -7.918 3.494 -6.975 -7.717 -4.266 -7.912 -6.303 1.648 -8.123 -3.772 -6.505 + ML 106 104 6 109 6 1 1 22 41 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 107 104 6 109 6 1 1 22 41 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 108 104 6 109 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 109 109 5 109 6 1 1 23 41 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 110 110 6 110 5 1 1 22 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 34 ] 9 18 U A - - + MP 111 110 6 115 6 2 2 21 39 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -7.836 -7.795 -7.436 -3.794 -5.957 -7.798 2.220 -6.790 -7.445 1.323 -7.710 -5.649 3.103 -7.832 -3.590 -6.217 + ML 112 110 6 115 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 113 110 6 115 6 1 1 21 40 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 114 110 6 115 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 115 115 5 115 6 1 1 21 40 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 116 116 6 116 5 1 1 21 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 35 ] 10 17 C G - - + MP 117 116 6 121 6 2 2 19 37 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -8.021 -8.050 -7.554 -4.088 -6.028 -7.856 3.184 -6.884 -7.587 0.019 -7.815 -5.994 2.506 -7.979 -3.679 -6.365 + ML 118 116 6 121 6 1 1 21 39 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 119 116 6 121 6 1 1 20 39 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 120 116 6 121 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 121 121 5 121 6 1 1 20 39 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 122 122 6 122 5 1 1 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 36 ] 11 16 U A - - + MP 123 122 6 127 4 2 2 17 35 -10.705 -10.912 -0.004 -9.326 -8.498 -8.756 -7.833 -4.969 -6.193 -7.989 1.976 -7.104 -7.931 -4.927 -8.060 -7.105 3.379 -8.342 0.623 -6.731 + ML 124 122 6 127 4 1 1 20 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 + MR 125 122 6 127 4 1 1 20 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 + D 126 122 6 127 4 0 0 19 37 -4.568 -4.250 -2.265 -0.520 + IL 127 127 5 127 4 1 1 22 40 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 + IR 128 128 6 128 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 37 ] 12 - U - - - + ML 129 128 6 131 3 1 1 14 32 -11.622 -0.002 -10.276 0.104 -1.394 -4.333 1.319 + D 130 128 6 131 3 0 0 16 34 -6.174 -1.687 -0.566 + IL 131 131 3 131 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 38 ] 13 - U - - - + ML 132 131 3 134 3 1 1 12 31 -11.622 -0.002 -10.276 -2.505 0.463 -5.033 1.272 + D 133 131 3 134 3 0 0 15 33 -6.174 -1.687 -0.566 + IL 134 134 3 134 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 39 ] 14 - U - - - + ML 135 134 3 137 3 1 1 11 29 -11.622 -0.002 -10.276 -7.616 -6.858 -8.607 1.994 + D 136 134 3 137 3 0 0 13 32 -6.174 -1.687 -0.566 + IL 137 137 3 137 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 40 ] 15 - a - - - + ML 138 137 3 140 2 1 1 1 1 * 0.000 0.741 0.478 -2.313 -0.445 + D 139 137 3 140 2 0 0 0 0 * 0.000 + IL 140 140 3 140 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 + [ END 41 ] - - - - - - + E 141 140 3 -1 0 0 0 0 0 +// +HMMER3/f [3.3 | Nov 2019] +NAME Histone3 +ACC RF00032 +DESC Histone 3' UTR stem-loop +LENG 46 +MAXL 102 +ALPH RNA +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Fri Apr 4 13:03:46 2014 +COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED +NSEQ 46 +EFFN 42.133911 +CKSUM 471917655 +STATS LOCAL MSV -8.1088 0.74543 +STATS LOCAL VITERBI -8.5088 0.74543 +STATS LOCAL FORWARD -3.2029 0.74543 +HMM A C G U + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.16847 1.39084 1.71368 1.34673 + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 0.00000 * + 1 1.19718 0.92283 2.53752 1.50734 1 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 2 0.99976 0.91709 2.73454 1.78721 2 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 3 0.28707 2.15200 4.53977 2.09870 3 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 4 0.67303 1.40667 2.67938 1.73570 4 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 5 0.71631 0.93175 4.42267 2.24827 5 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 6 4.96323 6.10024 0.01150 6.11805 6 G - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 7 4.97477 6.07793 0.01151 6.10217 7 G - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 8 2.42219 0.35197 5.16373 1.59825 8 C - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 9 4.96709 1.22589 1.84282 0.61402 9 U - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 10 5.14332 0.56593 2.72176 1.02007 10 C - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 11 5.65512 1.39382 5.58556 0.29488 11 U - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 12 1.31706 2.34288 4.27893 0.47454 12 U - - _ + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 13 3.10136 1.06700 4.79001 0.50640 13 U - - _ + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 14 6.52235 6.01860 7.19543 0.00466 14 U - - _ + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 15 0.87615 1.05939 2.96086 1.68645 15 a - - _ + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 16 0.43199 5.71946 1.06961 5.43487 16 A - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 17 1.03329 2.73783 0.55849 4.90865 17 G - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 18 0.62348 1.85123 1.21052 4.72873 18 A - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 19 1.62037 5.32794 0.34630 2.40773 19 G - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 20 6.16935 0.01425 6.02393 4.64210 20 C - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 21 6.22221 0.03904 6.06094 3.38213 21 C - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 22 0.03027 3.82336 5.58493 5.47058 22 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 23 3.26053 0.29487 4.86483 1.56402 23 C - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 24 1.15929 0.76514 3.19669 1.71411 24 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.47612 0.97621 6.17794 0.01098 4.51736 1.09861 0.40547 + 25 0.90589 0.99871 2.78941 1.79574 26 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 26 0.37936 2.45545 2.76975 1.78857 27 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.03553 6.17794 3.41622 1.46634 0.26236 1.09861 0.40547 + 27 2.00288 0.98595 2.07379 1.00440 28 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00429 6.14670 6.14670 1.46634 0.26236 0.11900 2.18757 + 28 0.58277 2.57844 2.26067 1.34141 29 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 29 2.04103 1.64155 1.24300 0.94698 30 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.04224 6.17794 3.23682 1.46634 0.26236 1.09861 0.40547 + 30 0.90025 2.40010 2.48509 0.86868 31 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00432 6.14002 6.14002 1.46634 0.26236 0.10040 2.34838 + 31 1.14658 1.52988 1.97258 1.11897 32 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 32 0.99477 1.56394 2.34075 1.12508 33 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 33 1.30260 0.91111 1.74486 1.88763 34 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 34 0.81644 1.95418 2.55798 1.08218 35 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 35 0.88707 2.68494 1.54697 1.18084 36 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.02155 6.17794 3.95035 1.46634 0.26236 1.09861 0.40547 + 36 0.88692 1.97884 1.71659 1.30871 37 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00423 6.16062 6.16062 1.46634 0.26236 0.19522 1.72966 + 37 0.78649 1.68131 1.71782 1.72051 38 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 38 0.59588 2.08432 1.60986 2.08251 39 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 39 0.76886 1.58017 1.51684 2.19720 40 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.02859 6.17794 3.64554 1.46634 0.26236 1.09861 0.40547 + 40 0.91147 2.90974 1.18115 1.44117 41 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00426 6.15362 6.15362 1.46634 0.26236 0.14750 1.98676 + 41 1.19023 1.82584 1.84655 0.97555 42 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 42 1.35396 2.21010 1.23260 1.07716 43 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 43 1.25472 1.71330 1.50591 1.16232 44 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 44 1.37043 1.66018 2.98397 0.68259 45 U - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 45 1.15612 1.70216 1.15511 1.67140 46 g - - : + 1.38629 1.38629 1.38629 1.38629 + 0.47997 6.17794 0.96989 1.46634 0.26236 1.09861 0.40547 + 46 2.25321 3.55314 1.66807 0.38906 47 U - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00335 5.70132 * 1.46634 0.26236 0.00000 * +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/comparison_stats.rbpbench_compare.test.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,5 @@ +combined_id method_id data_id motif_db rbp_id c_regions c_uniq_motif_hits perc_reg_with_hits perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt +k562_eclip,human_v0.1,PUM1 dewseq_w100_s5 k562_eclip human_v0.1 PUM1 23 24 43.47826086956522 3.2 4.859283255719781 +k562_eclip,human_v0.1,PUM1 clipper_idr k562_eclip human_v0.1 PUM1 32 8 18.75 2.691013935607881 3.8443056222969725 +k562_eclip,human_v0.1,PUM2 dewseq_w100_s5 k562_eclip human_v0.1 PUM2 70 448 92.85714285714286 14.084164436876673 31.46288362946836 +k562_eclip,human_v0.1,PUM2 clipper_idr k562_eclip human_v0.1 PUM2 77 219 76.62337662337663 17.64076214943267 46.88503532434168
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contingency_table_results.rbpbench_search.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,3 @@ +#rbp_id PUM1 PUM2 +PUM1 1.0 1.0 +PUM2 1.0 1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa +testid testdbkey testdisplay ${__HERE__}/test.fa \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_sites.filtered.rbpbench_search.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,1 @@ +chr1 10 80 chr1:10-80(+) 0.0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_sites.filtered.rbpbench_search.fa Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,2 @@ +>chr1:10-80(+) +ACTGGTTGTGATTTGTAGATACTGGCTCTTCTCAGATGAAGTTCCAGGATTATTCATTGAAAAAGGCTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.compare_test.clipper_idr.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,228 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +k562_eclip clipper_idr run_id human_v0.1 chr21:43687539-43687632(+) PUM1 PUM1_1 chr21 43687623 43687629 + 84 90 93 1 9.0101 0.000415 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 chr21:8397346-8397397(+) PUM1 PUM1_1 chr21 8397362 8397368 + 16 22 51 1 12.1616 5.85e-05 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 chr21:8215025-8215091(+) PUM1 PUM1_1 chr21 8215042 8215048 + 17 23 66 1 6.9798 0.000768 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 chr21:8215025-8215091(+) PUM1 PUM1_1 chr21 8215045 8215051 + 20 26 66 1 11.1515 0.000238 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 chr21:8215025-8215091(+) PUM1 PUM1_1 chr21 8215075 8215081 + 50 56 66 1 11.1515 0.000238 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 chr21:8214310-8214363(+) PUM1 PUM1_1 chr21 8214324 8214330 + 14 20 53 1 12.1616 5.85e-05 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 chr21:36375568-36375657(+) PUM1 PUM1_2 chr21 36375632 36375640 + 64 72 89 1 -2.35354 0.000906 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 chr21:32764345-32764372(-) PUM1 PUM1_2 chr21 32764358 32764366 - 7 15 27 1 6.31313 0.000191 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 chr21:14371121-14371193(-) PUM2 PUM2_1 chr21 14371170 14371177 - 17 24 72 1 4.78788 0.000283 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14371121-14371193(-) PUM2 PUM2_1 chr21 14371168 14371175 - 19 26 72 1 4.69697 0.000481 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14371121-14371193(-) PUM2 PUM2_1 chr21 14371143 14371150 - 44 51 72 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734876-32734935(-) PUM2 PUM2_1 chr21 32734896 32734903 - 33 40 59 1 11.8788 8.1e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734876-32734935(-) PUM2 PUM2_1 chr21 32734887 32734894 - 42 49 59 1 14.3636 1.62e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32733994-32734078(-) PUM2 PUM2_1 chr21 32734055 32734062 - 17 24 84 1 4.78788 0.000283 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32733994-32734078(-) PUM2 PUM2_1 chr21 32734041 32734048 - 31 38 84 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961306-14961341(-) PUM2 PUM2_1 chr21 14961325 14961332 - 10 17 35 1 12.9798 4.95e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:28945887-28945953(-) PUM2 PUM2_1 chr21 28945911 28945918 - 36 43 66 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576734-33576815(+) PUM2 PUM2_1 chr21 33576754 33576761 + 20 27 81 1 4.78788 0.000283 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576651-33576714(+) PUM2 PUM2_1 chr21 33576671 33576678 + 20 27 63 1 4.54545 0.000789 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576651-33576714(+) PUM2 PUM2_1 chr21 33576685 33576692 + 34 41 63 1 4.54545 0.000789 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576604-33576651(+) PUM2 PUM2_1 chr21 33576643 33576650 + 39 46 47 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36376271-36376367(+) PUM2 PUM2_1 chr21 36376310 36376317 + 39 46 96 1 14.3636 1.62e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36376271-36376367(+) PUM2 PUM2_1 chr21 36376312 36376319 + 41 48 96 1 4.71717 0.000332 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37223448-37223498(-) PUM2 PUM2_1 chr21 37223459 37223466 - 33 40 50 1 12.0303 6.48e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37202978-37203044(+) PUM2 PUM2_1 chr21 37203027 37203034 + 49 56 66 1 12.9798 4.95e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:46569364-46569436(+) PUM2 PUM2_1 chr21 46569382 46569389 + 18 25 72 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36375540-36375560(+) PUM2 PUM2_1 chr21 36375544 36375551 + 4 11 20 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33560587-33560651(+) PUM2 PUM2_1 chr21 33560605 33560612 + 18 25 64 1 4.78788 0.000283 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485722-14485766(-) PUM2 PUM2_1 chr21 14485730 14485737 - 30 37 44 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485656-14485707(-) PUM2 PUM2_1 chr21 14485692 14485699 - 9 16 51 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:17788991-17789050(-) PUM2 PUM2_1 chr21 17789024 17789031 - 20 27 59 1 14.3636 1.62e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:45602682-45602742(+) PUM2 PUM2_1 chr21 45602699 45602706 + 17 24 60 1 12.0303 6.48e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:45602682-45602742(+) PUM2 PUM2_1 chr21 45602733 45602740 + 51 58 60 1 4.87879 0.000191 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37515039-37515108(+) PUM2 PUM2_1 chr21 37515084 37515091 + 45 52 69 1 4.78788 0.000283 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37515039-37515108(+) PUM2 PUM2_1 chr21 37515086 37515093 + 47 54 69 1 12.0303 6.48e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32628790-32628839(-) PUM2 PUM2_1 chr21 32628809 32628816 - 24 31 49 1 12.9798 4.95e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:43760985-43761109(+) PUM2 PUM2_1 chr21 43761044 43761051 + 59 66 124 1 12.0303 6.48e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:46324135-46324199(+) PUM2 PUM2_1 chr21 46324158 46324165 + 23 30 64 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:29345202-29345237(+) PUM2 PUM2_1 chr21 29345209 29345216 + 7 14 35 1 12.0303 6.48e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_1 chr21 34099722 34099729 + 25 32 86 1 4.78788 0.000283 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_1 chr21 34099724 34099731 + 27 34 86 1 14.3636 1.62e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_1 chr21 34099762 34099769 + 65 72 86 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:39175479-39175597(-) PUM2 PUM2_1 chr21 39175562 39175569 - 29 36 118 1 12.0303 6.48e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:39175479-39175597(-) PUM2 PUM2_1 chr21 39175515 39175522 - 76 83 118 1 8.07071 0.000128 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34791774-34791828(-) PUM2 PUM2_1 chr21 34791779 34791786 - 43 50 54 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33524027-33524134(-) PUM2 PUM2_1 chr21 33524100 33524107 - 28 35 107 1 4.78788 0.000283 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:38156408-38156501(+) PUM2 PUM2_1 chr21 38156461 38156468 + 53 60 93 1 10.6465 9.62e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:38823652-38823706(+) PUM2 PUM2_1 chr21 38823684 38823691 + 32 39 54 1 10.6465 9.62e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437436-33437487(+) PUM2 PUM2_1 chr21 33437440 33437447 + 4 11 51 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437328-33437436(+) PUM2 PUM2_1 chr21 33437400 33437407 + 72 79 108 1 3.64646 0.000819 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437328-33437436(+) PUM2 PUM2_1 chr21 33437428 33437435 + 100 107 108 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961795-14961851(-) PUM2 PUM2_1 chr21 14961842 14961849 - 3 10 56 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961795-14961851(-) PUM2 PUM2_1 chr21 14961807 14961814 - 38 45 56 1 4.78788 0.000283 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961795-14961851(-) PUM2 PUM2_1 chr21 14961803 14961810 - 42 49 56 1 4.69697 0.000481 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961851-14961895(-) PUM2 PUM2_1 chr21 14961861 14961868 - 28 35 44 1 12.0303 6.48e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36376401-36376460(+) PUM2 PUM2_1 chr21 36376422 36376429 + 21 28 59 1 4.78788 0.000283 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:29326164-29326210(+) PUM2 PUM2_1 chr21 29326166 29326173 + 2 9 46 1 12.9798 4.95e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44861160-44861215(-) PUM2 PUM2_1 chr21 44861192 44861199 - 17 24 55 1 11.8788 8.1e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485244-14485280(-) PUM2 PUM2_1 chr21 14485254 14485261 - 20 27 36 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485280-14485326(-) PUM2 PUM2_1 chr21 14485285 14485292 - 35 42 46 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34105575-34105653(+) PUM2 PUM2_1 chr21 34105602 34105609 + 27 34 78 1 12.0303 6.48e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34105575-34105653(+) PUM2 PUM2_1 chr21 34105611 34105618 + 36 43 78 1 3.64646 0.000819 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34098703-34098750(+) PUM2 PUM2_1 chr21 34098705 34098712 + 2 9 47 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734633-32734683(-) PUM2 PUM2_1 chr21 32734647 32734654 - 30 37 50 1 11.8788 8.1e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734633-32734683(-) PUM2 PUM2_1 chr21 32734638 32734645 - 39 46 50 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44805626-44805677(-) PUM2 PUM2_1 chr21 44805668 44805675 - 3 10 51 1 10.6465 9.62e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44805626-44805677(-) PUM2 PUM2_1 chr21 44805641 44805648 - 30 37 51 1 4.54545 0.000789 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44805626-44805677(-) PUM2 PUM2_1 chr21 44805634 44805641 - 37 44 51 1 4.54545 0.000789 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37513867-37513939(+) PUM2 PUM2_1 chr21 37513892 37513899 + 25 32 72 1 4.63636 0.000578 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961937-14961964(-) PUM2 PUM2_1 chr21 14961945 14961952 - 13 20 27 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_1 chr21 34887732 34887739 - 18 25 78 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_1 chr21 34887705 34887712 - 45 52 78 1 14.3636 1.62e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_1 chr21 34887697 34887704 - 53 60 78 1 4.71717 0.000332 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_1 chr21 34887695 34887702 - 55 62 78 1 4.71717 0.000332 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33578030-33578124(-) PUM2 PUM2_1 chr21 33578071 33578078 - 47 54 94 1 12.0303 6.48e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:43983033-43983127(+) PUM2 PUM2_1 chr21 43983059 43983066 + 26 33 94 1 14.2121 3.34e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961306-14961341(-) PUM2 PUM2_2 chr21 14961325 14961332 - 10 17 35 1 6.30303 0.000377 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33504132-33504209(-) PUM2 PUM2_2 chr21 33504165 33504172 - 38 45 77 1 6.31313 0.000284 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576604-33576651(+) PUM2 PUM2_2 chr21 33576612 33576619 + 8 15 47 1 -3.24242 0.000754 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37202978-37203044(+) PUM2 PUM2_2 chr21 37203027 37203034 + 49 56 66 1 6.30303 0.000377 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:45602682-45602742(+) PUM2 PUM2_2 chr21 45602708 45602715 + 26 33 60 1 6.31313 0.000284 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32628790-32628839(-) PUM2 PUM2_2 chr21 32628809 32628816 - 24 31 49 1 6.30303 0.000377 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_2 chr21 34099702 34099709 + 5 12 86 1 6.31313 0.000284 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:38156408-38156501(+) PUM2 PUM2_2 chr21 38156461 38156468 + 53 60 93 1 6.30303 0.000377 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:38823652-38823706(+) PUM2 PUM2_2 chr21 38823684 38823691 + 32 39 54 1 6.30303 0.000377 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437328-33437436(+) PUM2 PUM2_2 chr21 33437400 33437407 + 72 79 108 1 15.9798 1.5e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:29326164-29326210(+) PUM2 PUM2_2 chr21 29326166 29326173 + 2 9 46 1 6.30303 0.000377 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34105575-34105653(+) PUM2 PUM2_2 chr21 34105611 34105618 + 36 43 78 1 6.30303 0.000377 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44805626-44805677(-) PUM2 PUM2_2 chr21 44805668 44805675 - 3 10 51 1 6.30303 0.000377 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961257-14961282(-) PUM2 PUM2_2 chr21 14961274 14961281 - 2 9 25 1 -3.24242 0.000754 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36375329-36375363(+) PUM2 PUM2_2 chr21 36375341 36375348 + 12 19 34 1 6.31313 0.000284 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:43983033-43983127(+) PUM2 PUM2_2 chr21 43983067 43983074 + 34 41 94 1 6.31313 0.000284 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14371121-14371193(-) PUM2 PUM2_3 chr21 14371143 14371150 - 44 51 72 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734876-32734935(-) PUM2 PUM2_3 chr21 32734896 32734903 - 33 40 59 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734876-32734935(-) PUM2 PUM2_3 chr21 32734887 32734894 - 42 49 59 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32733994-32734078(-) PUM2 PUM2_3 chr21 32734041 32734048 - 31 38 84 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961306-14961341(-) PUM2 PUM2_3 chr21 14961325 14961332 - 10 17 35 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:28945887-28945953(-) PUM2 PUM2_3 chr21 28945911 28945918 - 36 43 66 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576651-33576714(+) PUM2 PUM2_3 chr21 33576671 33576678 + 20 27 63 1 6.11111 0.000423 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576651-33576714(+) PUM2 PUM2_3 chr21 33576685 33576692 + 34 41 63 1 6.11111 0.000423 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576604-33576651(+) PUM2 PUM2_3 chr21 33576643 33576650 + 39 46 47 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36376271-36376367(+) PUM2 PUM2_3 chr21 36376310 36376317 + 39 46 96 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37202978-37203044(+) PUM2 PUM2_3 chr21 37203027 37203034 + 49 56 66 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:46569364-46569436(+) PUM2 PUM2_3 chr21 46569382 46569389 + 18 25 72 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36375540-36375560(+) PUM2 PUM2_3 chr21 36375544 36375551 + 4 11 20 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485722-14485766(-) PUM2 PUM2_3 chr21 14485730 14485737 - 30 37 44 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485656-14485707(-) PUM2 PUM2_3 chr21 14485692 14485699 - 9 16 51 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:17788991-17789050(-) PUM2 PUM2_3 chr21 17789024 17789031 - 20 27 59 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:45602682-45602742(+) PUM2 PUM2_3 chr21 45602733 45602740 + 51 58 60 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32628790-32628839(-) PUM2 PUM2_3 chr21 32628809 32628816 - 24 31 49 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:46324135-46324199(+) PUM2 PUM2_3 chr21 46324158 46324165 + 23 30 64 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_3 chr21 34099724 34099731 + 27 34 86 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_3 chr21 34099762 34099769 + 65 72 86 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34791774-34791828(-) PUM2 PUM2_3 chr21 34791779 34791786 - 43 50 54 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437436-33437487(+) PUM2 PUM2_3 chr21 33437440 33437447 + 4 11 51 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437328-33437436(+) PUM2 PUM2_3 chr21 33437428 33437435 + 100 107 108 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961795-14961851(-) PUM2 PUM2_3 chr21 14961842 14961849 - 3 10 56 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:29326164-29326210(+) PUM2 PUM2_3 chr21 29326166 29326173 + 2 9 46 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44861160-44861215(-) PUM2 PUM2_3 chr21 44861192 44861199 - 17 24 55 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485244-14485280(-) PUM2 PUM2_3 chr21 14485254 14485261 - 20 27 36 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485280-14485326(-) PUM2 PUM2_3 chr21 14485285 14485292 - 35 42 46 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34098703-34098750(+) PUM2 PUM2_3 chr21 34098705 34098712 + 2 9 47 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734633-32734683(-) PUM2 PUM2_3 chr21 32734647 32734654 - 30 37 50 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734633-32734683(-) PUM2 PUM2_3 chr21 32734638 32734645 - 39 46 50 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44805626-44805677(-) PUM2 PUM2_3 chr21 44805641 44805648 - 30 37 51 1 6.11111 0.000423 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44805626-44805677(-) PUM2 PUM2_3 chr21 44805634 44805641 - 37 44 51 1 6.11111 0.000423 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37513867-37513939(+) PUM2 PUM2_3 chr21 37513892 37513899 + 25 32 72 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961937-14961964(-) PUM2 PUM2_3 chr21 14961945 14961952 - 13 20 27 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_3 chr21 34887732 34887739 - 18 25 78 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_3 chr21 34887705 34887712 - 45 52 78 1 6.20202 0.000212 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:43983033-43983127(+) PUM2 PUM2_3 chr21 43983059 43983066 + 26 33 94 1 15.7778 1.72e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14371121-14371193(-) PUM2 PUM2_4 chr21 14371143 14371150 - 44 51 72 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734876-32734935(-) PUM2 PUM2_4 chr21 32734887 32734894 - 42 49 59 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32733994-32734078(-) PUM2 PUM2_4 chr21 32734041 32734048 - 31 38 84 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961306-14961341(-) PUM2 PUM2_4 chr21 14961325 14961332 - 10 17 35 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:28945887-28945953(-) PUM2 PUM2_4 chr21 28945911 28945918 - 36 43 66 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576604-33576651(+) PUM2 PUM2_4 chr21 33576643 33576650 + 39 46 47 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36376271-36376367(+) PUM2 PUM2_4 chr21 36376310 36376317 + 39 46 96 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37202978-37203044(+) PUM2 PUM2_4 chr21 37203027 37203034 + 49 56 66 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:17788991-17789050(-) PUM2 PUM2_4 chr21 17789024 17789031 - 20 27 59 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32628790-32628839(-) PUM2 PUM2_4 chr21 32628809 32628816 - 24 31 49 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:46324135-46324199(+) PUM2 PUM2_4 chr21 46324158 46324165 + 23 30 64 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_4 chr21 34099724 34099731 + 27 34 86 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_4 chr21 34099762 34099769 + 65 72 86 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:39175479-39175597(-) PUM2 PUM2_4 chr21 39175515 39175522 - 76 83 118 1 6.27273 0.000156 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33524027-33524134(-) PUM2 PUM2_4 chr21 33524055 33524062 - 73 80 107 1 -3.30303 0.0008 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437436-33437487(+) PUM2 PUM2_4 chr21 33437440 33437447 + 4 11 51 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961795-14961851(-) PUM2 PUM2_4 chr21 14961842 14961849 - 3 10 56 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:29326164-29326210(+) PUM2 PUM2_4 chr21 29326166 29326173 + 2 9 46 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:29326125-29326164(+) PUM2 PUM2_4 chr21 29326130 29326137 + 5 12 39 1 -3.30303 0.0008 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485280-14485326(-) PUM2 PUM2_4 chr21 14485285 14485292 - 35 42 46 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961937-14961964(-) PUM2 PUM2_4 chr21 14961945 14961952 - 13 20 27 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_4 chr21 34887732 34887739 - 18 25 78 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_4 chr21 34887705 34887712 - 45 52 78 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:43983033-43983127(+) PUM2 PUM2_4 chr21 43983059 43983066 + 26 33 94 1 6.20202 0.000255 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14371121-14371193(-) PUM2 PUM2_5 chr21 14371170 14371179 - 15 24 72 1 8.27273 0.000508 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14371121-14371193(-) PUM2 PUM2_5 chr21 14371143 14371152 - 42 51 72 1 11.9293 4.81e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734876-32734935(-) PUM2 PUM2_5 chr21 32734896 32734905 - 31 40 59 1 11.4545 6.81e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734876-32734935(-) PUM2 PUM2_5 chr21 32734887 32734896 - 40 49 59 1 14.7071 9.81e-07 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734876-32734935(-) PUM2 PUM2_5 chr21 32734885 32734894 - 42 51 59 1 7.45455 0.000727 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734876-32734935(-) PUM2 PUM2_5 chr21 32734879 32734888 - 48 57 59 1 10.2323 0.000167 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32733994-32734078(-) PUM2 PUM2_5 chr21 32734041 32734050 - 29 38 84 1 12.7172 2.11e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961306-14961341(-) PUM2 PUM2_5 chr21 14961325 14961334 - 8 17 35 1 11.6566 6.11e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:28945887-28945953(-) PUM2 PUM2_5 chr21 28945911 28945920 - 34 43 66 1 10.0303 0.000196 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576734-33576815(+) PUM2 PUM2_5 chr21 33576754 33576763 + 20 29 81 1 7.64646 0.000672 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33504132-33504209(-) PUM2 PUM2_5 chr21 33504165 33504174 - 36 45 77 1 6.72727 0.000983 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576651-33576714(+) PUM2 PUM2_5 chr21 33576669 33576678 + 18 27 63 1 9.56566 0.000256 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576651-33576714(+) PUM2 PUM2_5 chr21 33576683 33576692 + 32 41 63 1 9.54545 0.00026 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33576604-33576651(+) PUM2 PUM2_5 chr21 33576641 33576650 + 37 46 47 1 11.6263 6.33e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36376271-36376367(+) PUM2 PUM2_5 chr21 36376308 36376317 + 37 46 96 1 13.9192 3.92e-06 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36376271-36376367(+) PUM2 PUM2_5 chr21 36376310 36376319 + 39 48 96 1 9.43434 0.00027 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36376271-36376367(+) PUM2 PUM2_5 chr21 36376343 36376352 + 72 81 96 1 6.92929 0.000923 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37223448-37223498(-) PUM2 PUM2_5 chr21 37223459 37223468 - 31 40 50 1 11.0606 9.24e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37202978-37203044(+) PUM2 PUM2_5 chr21 37203025 37203034 + 47 56 66 1 14.3232 1.95e-06 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:46569364-46569436(+) PUM2 PUM2_5 chr21 46569388 46569397 + 24 33 72 1 11.5051 6.62e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36375540-36375560(+) PUM2 PUM2_5 chr21 36375542 36375551 + 2 11 20 1 10.101 0.000188 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36375651-36375701(+) PUM2 PUM2_5 chr21 36375655 36375664 + 4 13 50 1 7.67677 0.000661 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:17788991-17789050(-) PUM2 PUM2_5 chr21 17789024 17789033 - 18 27 59 1 12.0404 4.11e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:17788991-17789050(-) PUM2 PUM2_5 chr21 17789022 17789031 - 20 29 59 1 7.45455 0.000727 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:45602682-45602742(+) PUM2 PUM2_5 chr21 45602697 45602706 + 15 24 60 1 12.1515 3.69e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:45602682-45602742(+) PUM2 PUM2_5 chr21 45602706 45602715 + 24 33 60 1 7.77778 0.00064 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:45602682-45602742(+) PUM2 PUM2_5 chr21 45602731 45602740 + 49 58 60 1 10.1717 0.000174 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37515108-37515163(+) PUM2 PUM2_5 chr21 37515122 37515131 + 14 23 55 1 7.71717 0.000655 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37515039-37515108(+) PUM2 PUM2_5 chr21 37515084 37515093 + 45 54 69 1 12.3939 2.8e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32628790-32628839(-) PUM2 PUM2_5 chr21 32628809 32628818 - 22 31 49 1 12.7071 2.2e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:43760985-43761109(+) PUM2 PUM2_5 chr21 43761042 43761051 + 57 66 124 1 12.1515 3.69e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:46324135-46324199(+) PUM2 PUM2_5 chr21 46324156 46324165 + 21 30 64 1 11.1212 8.74e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:29345202-29345237(+) PUM2 PUM2_5 chr21 29345207 29345216 + 5 14 35 1 12.3737 2.89e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_5 chr21 34099720 34099729 + 23 32 86 1 8.27273 0.000508 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_5 chr21 34099722 34099731 + 25 34 86 1 13.1111 1.1e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34099697-34099783(+) PUM2 PUM2_5 chr21 34099760 34099769 + 63 72 86 1 12.1515 3.69e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:39175479-39175597(-) PUM2 PUM2_5 chr21 39175562 39175571 - 27 36 118 1 11.3434 7.4e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:39175479-39175597(-) PUM2 PUM2_5 chr21 39175515 39175524 - 74 83 118 1 10.1616 0.000175 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33524027-33524134(-) PUM2 PUM2_5 chr21 33524083 33524092 - 43 52 107 1 8.48485 0.000453 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33524027-33524134(-) PUM2 PUM2_5 chr21 33524047 33524056 - 79 88 107 1 10.9293 0.000107 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33524027-33524134(-) PUM2 PUM2_5 chr21 33524030 33524039 - 96 105 107 1 8.61616 0.000424 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:38156408-38156501(+) PUM2 PUM2_5 chr21 38156459 38156468 + 51 60 93 1 11.7677 5.5e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:43693414-43693454(+) PUM2 PUM2_5 chr21 43693415 43693424 + 1 10 40 1 12.2929 3.08e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:43693369-43693414(+) PUM2 PUM2_5 chr21 43693399 43693408 + 30 39 45 1 7.35354 0.00076 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:38823652-38823706(+) PUM2 PUM2_5 chr21 38823682 38823691 + 30 39 54 1 13.6061 6.92e-06 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437436-33437487(+) PUM2 PUM2_5 chr21 33437438 33437447 + 2 11 51 1 11.9394 4.69e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437328-33437436(+) PUM2 PUM2_5 chr21 33437398 33437407 + 70 79 108 1 8.80808 0.000397 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33437328-33437436(+) PUM2 PUM2_5 chr21 33437426 33437435 + 98 107 108 1 8.26263 0.000513 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961795-14961851(-) PUM2 PUM2_5 chr21 14961842 14961851 - 1 10 56 1 11.1212 8.74e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961851-14961895(-) PUM2 PUM2_5 chr21 14961861 14961870 - 26 35 44 1 10.5455 0.000137 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:45512384-45512556(+) PUM2 PUM2_5 chr21 45512511 45512520 + 127 136 172 1 8.51515 0.000442 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33558801-33558874(+) PUM2 PUM2_5 chr21 33558832 33558841 + 31 40 73 1 7.71717 0.000655 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44861160-44861215(-) PUM2 PUM2_5 chr21 44861192 44861201 - 15 24 55 1 13.0505 1.29e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14485280-14485326(-) PUM2 PUM2_5 chr21 14485285 14485294 - 33 42 46 1 11.1212 8.74e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34105575-34105653(+) PUM2 PUM2_5 chr21 34105600 34105609 + 25 34 78 1 10.2525 0.000164 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34105575-34105653(+) PUM2 PUM2_5 chr21 34105609 34105618 + 34 43 78 1 10.7475 0.000121 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734633-32734683(-) PUM2 PUM2_5 chr21 32734647 32734656 - 28 37 50 1 10.404 0.000149 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734633-32734683(-) PUM2 PUM2_5 chr21 32734638 32734647 - 37 46 50 1 8.50505 0.000445 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:44805626-44805677(-) PUM2 PUM2_5 chr21 44805668 44805677 - 1 10 51 1 13.6061 6.92e-06 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:37513867-37513939(+) PUM2 PUM2_5 chr21 37513905 37513914 + 38 47 72 1 7.0404 0.000882 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:14961937-14961964(-) PUM2 PUM2_5 chr21 14961945 14961954 - 11 20 27 1 10.8384 0.000118 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:32734837-32734876(-) PUM2 PUM2_5 chr21 32734862 32734871 - 6 15 39 1 7.77778 0.00064 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_5 chr21 34887737 34887746 - 11 20 78 1 7.24242 0.000807 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_5 chr21 34887732 34887741 - 16 25 78 1 12.7172 2.11e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_5 chr21 34887705 34887714 - 43 52 78 1 13.9192 3.92e-06 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_5 chr21 34887703 34887712 - 45 54 78 1 8.71717 0.000411 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_5 chr21 34887697 34887706 - 51 60 78 1 9.17172 0.00032 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:34887678-34887756(-) PUM2 PUM2_5 chr21 34887695 34887704 - 53 62 78 1 11.0303 9.55e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:36375329-36375363(+) PUM2 PUM2_5 chr21 36375339 36375348 + 10 19 34 1 7.25253 0.000803 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:33578030-33578124(-) PUM2 PUM2_5 chr21 33578071 33578080 - 45 54 94 1 12.9394 1.5e-05 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:31671330-31671381(-) PUM2 PUM2_5 chr21 31671335 31671344 - 38 47 51 1 8.55556 0.000433 - - AJ40lTA6 +k562_eclip clipper_idr run_id human_v0.1 chr21:43983033-43983127(+) PUM2 PUM2_5 chr21 43983057 43983066 + 24 33 94 1 12.1717 3.39e-05 - - AJ40lTA6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.compare_test.dewseq.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,584 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8214212-8214407(+) PUM1 PUM1_1 chr21 8214298 8214304 + 86 92 195 1 8.83838 0.000473 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8214212-8214407(+) PUM1 PUM1_1 chr21 8214324 8214330 + 112 118 195 1 12.1616 5.85e-05 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8218652-8218957(+) PUM1 PUM1_1 chr21 8218698 8218704 + 46 52 305 1 11.3232 0.00018 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8213907-8214127(+) PUM1 PUM1_1 chr21 8214075 8214081 + 168 174 220 1 6.9798 0.000768 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8217782-8218632(+) PUM1 PUM1_1 chr21 8217841 8217847 + 59 65 850 1 6.9798 0.000768 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8217782-8218632(+) PUM1 PUM1_1 chr21 8217884 8217890 + 102 108 850 1 11.1515 0.000238 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8217782-8218632(+) PUM1 PUM1_1 chr21 8217961 8217967 + 179 185 850 1 11.3232 0.00018 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8217782-8218632(+) PUM1 PUM1_1 chr21 8217962 8217968 + 180 186 850 1 6.9798 0.000768 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8401688-8401913(+) PUM1 PUM1_1 chr21 8401737 8401743 + 49 55 225 1 11.3232 0.00018 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397503-8397723(+) PUM1 PUM1_1 chr21 8397514 8397520 + 11 17 220 1 11.1515 0.000238 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397503-8397723(+) PUM1 PUM1_1 chr21 8397534 8397540 + 31 37 220 1 9.0101 0.000415 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397503-8397723(+) PUM1 PUM1_1 chr21 8397536 8397542 + 33 39 220 1 12.1616 5.85e-05 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397503-8397723(+) PUM1 PUM1_1 chr21 8397540 8397546 + 37 43 220 1 11.1515 0.000238 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397503-8397723(+) PUM1 PUM1_1 chr21 8397544 8397550 + 41 47 220 1 11.1515 0.000238 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397503-8397723(+) PUM1 PUM1_1 chr21 8397554 8397560 + 51 57 220 1 9.0101 0.000415 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397503-8397723(+) PUM1 PUM1_1 chr21 8397556 8397562 + 53 59 220 1 12.1616 5.85e-05 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397503-8397723(+) PUM1 PUM1_1 chr21 8397680 8397686 + 177 183 220 1 6.9798 0.000768 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397243-8397453(+) PUM1 PUM1_1 chr21 8397336 8397342 + 93 99 210 1 8.83838 0.000473 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:8397243-8397453(+) PUM1 PUM1_1 chr21 8397362 8397368 + 119 125 210 1 12.1616 5.85e-05 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43687515-43687745(+) PUM1 PUM1_1 chr21 43687623 43687629 + 108 114 230 1 9.0101 0.000415 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32764357-32764462(-) PUM1 PUM1_2 chr21 32764358 32764366 - 97 105 105 1 6.31313 0.000191 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375527-36375647(+) PUM1 PUM1_2 chr21 36375632 36375640 + 105 113 120 1 -2.35354 0.000906 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375527-36375647(+) PUM1 PUM1_3 chr21 36375534 36375541 + 7 14 120 1 12.5354 6.6e-05 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375527-36375647(+) PUM1 PUM1_3 chr21 36375556 36375563 + 29 36 120 1 4.61616 0.000739 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:5240799-5240909(-) PUM2 PUM2_1 chr21 5240861 5240868 - 42 49 110 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_1 chr21 14371383 14371390 - 50 57 325 1 10.6465 9.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_1 chr21 14371233 14371240 - 200 207 325 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_1 chr21 14371201 14371208 - 232 239 325 1 3.40404 0.00091 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_1 chr21 14371170 14371177 - 263 270 325 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_1 chr21 14371168 14371175 - 265 272 325 1 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_1 chr21 14371143 14371150 - 290 297 325 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_1 chr21 14485810 14485817 - 71 78 295 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_1 chr21 14485768 14485775 - 113 120 295 1 12.9798 4.95e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_1 chr21 14485730 14485737 - 151 158 295 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_1 chr21 14485692 14485699 - 189 196 295 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485227-14485462(-) PUM2 PUM2_1 chr21 14485285 14485292 - 171 178 235 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485227-14485462(-) PUM2 PUM2_1 chr21 14485254 14485261 - 202 209 235 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962128-14962318(-) PUM2 PUM2_1 chr21 14962220 14962227 - 92 99 190 2 10.404 0.000113 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961188-14961428(-) PUM2 PUM2_1 chr21 14961325 14961332 - 97 104 240 2 12.9798 4.95e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962047 14962054 - 5 12 405 2 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962038 14962045 - 14 21 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962036 14962043 - 16 23 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962034 14962041 - 18 25 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962032 14962039 - 20 27 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962030 14962037 - 22 29 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962028 14962035 - 24 31 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962026 14962033 - 26 33 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962024 14962031 - 28 35 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962022 14962029 - 30 37 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962020 14962027 - 32 39 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962018 14962025 - 34 41 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962016 14962023 - 36 43 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962005 14962012 - 47 54 405 2 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962003 14962010 - 49 56 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14962001 14962008 - 51 58 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14961999 14962006 - 53 60 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14961997 14962004 - 55 62 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14961945 14961952 - 107 114 405 2 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14961861 14961868 - 191 198 405 2 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14961842 14961849 - 210 217 405 2 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14961807 14961814 - 245 252 405 2 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14961803 14961810 - 249 256 405 2 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_1 chr21 14961777 14961784 - 275 282 405 2 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962047 14962054 - 6 13 405 2 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962038 14962045 - 15 22 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962036 14962043 - 17 24 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962034 14962041 - 19 26 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962032 14962039 - 21 28 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962030 14962037 - 23 30 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962028 14962035 - 25 32 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962026 14962033 - 27 34 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962024 14962031 - 29 36 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962022 14962029 - 31 38 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962020 14962027 - 33 40 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962018 14962025 - 35 42 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962016 14962023 - 37 44 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962005 14962012 - 48 55 405 2 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962003 14962010 - 50 57 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14962001 14962008 - 52 59 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14961999 14962006 - 54 61 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14961997 14962004 - 56 63 405 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14961945 14961952 - 108 115 405 2 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14961861 14961868 - 192 199 405 2 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14961842 14961849 - 211 218 405 2 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14961807 14961814 - 246 253 405 2 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14961803 14961810 - 250 257 405 2 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_1 chr21 14961777 14961784 - 276 283 405 2 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961234-14961429(-) PUM2 PUM2_1 chr21 14961325 14961332 - 98 105 195 2 12.9798 4.95e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962129-14962314(-) PUM2 PUM2_1 chr21 14962220 14962227 - 88 95 185 2 10.404 0.000113 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788950-17789135(-) PUM2 PUM2_1 chr21 17789055 17789062 - 74 81 185 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788950-17789135(-) PUM2 PUM2_1 chr21 17789024 17789031 - 105 112 185 2 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788966-17789136(-) PUM2 PUM2_1 chr21 17789055 17789062 - 75 82 170 2 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788966-17789136(-) PUM2 PUM2_1 chr21 17789024 17789031 - 106 113 170 2 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:28928288-28928403(-) PUM2 PUM2_1 chr21 28928381 28928388 - 16 23 115 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:28928288-28928403(-) PUM2 PUM2_1 chr21 28928377 28928384 - 20 27 115 1 12.9798 4.95e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29345143-29345258(+) PUM2 PUM2_1 chr21 29345209 29345216 + 66 73 115 1 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29345713-29345908(+) PUM2 PUM2_1 chr21 29345791 29345798 + 78 85 195 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29326058-29326273(+) PUM2 PUM2_1 chr21 29326166 29326173 + 108 115 215 1 12.9798 4.95e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:31668760-31668905(+) PUM2 PUM2_1 chr21 31668867 31668874 + 107 114 145 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:31671207-31671477(-) PUM2 PUM2_1 chr21 31671211 31671218 - 260 267 270 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32628758-32628913(-) PUM2 PUM2_1 chr21 32628809 32628816 - 98 105 155 1 12.9798 4.95e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_1 chr21 32734896 32734903 - 121 128 500 1 11.8788 8.1e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_1 chr21 32734887 32734894 - 130 137 500 1 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_1 chr21 32734647 32734654 - 370 377 500 1 11.8788 8.1e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_1 chr21 32734638 32734645 - 379 386 500 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_1 chr21 32734630 32734637 - 387 394 500 1 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_1 chr21 32734626 32734633 - 391 398 500 1 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32733913-32734158(-) PUM2 PUM2_1 chr21 32734055 32734062 - 97 104 245 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32733913-32734158(-) PUM2 PUM2_1 chr21 32734041 32734048 - 111 118 245 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32733913-32734158(-) PUM2 PUM2_1 chr21 32733935 32733942 - 217 224 245 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_1 chr21 33437400 33437407 + 163 170 284 1 3.64646 0.000819 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_1 chr21 33437428 33437435 + 191 198 284 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_1 chr21 33437440 33437447 + 203 210 284 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_1 chr21 33437481 33437488 + 244 251 284 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33450581-33450681(-) PUM2 PUM2_1 chr21 33450630 33450637 - 45 52 100 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33450581-33450681(-) PUM2 PUM2_1 chr21 33450622 33450629 - 53 60 100 1 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33524008-33524183(-) PUM2 PUM2_1 chr21 33524100 33524107 - 77 84 175 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_1 chr21 33576643 33576650 + 129 136 330 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_1 chr21 33576671 33576678 + 157 164 330 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_1 chr21 33576685 33576692 + 171 178 330 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_1 chr21 33576727 33576734 + 213 220 330 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_1 chr21 33576754 33576761 + 240 247 330 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33558740-33558910(+) PUM2 PUM2_1 chr21 33558894 33558901 + 154 161 170 1 5.0303 0.000159 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_1 chr21 33560567 33560574 + 66 73 166 1 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_1 chr21 33560569 33560576 + 68 75 166 1 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_1 chr21 33560577 33560584 + 76 83 166 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_1 chr21 33560583 33560590 + 82 89 166 1 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_1 chr21 33560585 33560592 + 84 91 166 1 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_1 chr21 33560587 33560594 + 86 93 166 1 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_1 chr21 33560605 33560612 + 104 111 166 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33577980-33578190(-) PUM2 PUM2_1 chr21 33578071 33578078 - 113 120 210 1 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105529-34105709(+) PUM2 PUM2_1 chr21 34105602 34105609 + 73 80 180 3 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105529-34105709(+) PUM2 PUM2_1 chr21 34105611 34105618 + 82 89 180 3 3.64646 0.000819 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34098610-34098805(+) PUM2 PUM2_1 chr21 34098705 34098712 + 95 102 195 2 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_1 chr21 34099722 34099729 + 62 69 165 2 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_1 chr21 34099724 34099731 + 64 71 165 2 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_1 chr21 34099762 34099769 + 102 109 165 2 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34142892-34143034(+) PUM2 PUM2_1 chr21 34142958 34142965 + 66 73 142 2 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34142890-34143080(+) PUM2 PUM2_1 chr21 34142958 34142965 + 68 75 190 2 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105530-34105710(+) PUM2 PUM2_1 chr21 34105602 34105609 + 72 79 180 3 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105530-34105710(+) PUM2 PUM2_1 chr21 34105611 34105618 + 81 88 180 3 3.64646 0.000819 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100020-34100120(+) PUM2 PUM2_1 chr21 34100074 34100081 + 54 61 100 2 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100020-34100120(+) PUM2 PUM2_1 chr21 34100076 34100083 + 56 63 100 2 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100017-34100122(+) PUM2 PUM2_1 chr21 34100074 34100081 + 57 64 105 2 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100017-34100122(+) PUM2 PUM2_1 chr21 34100076 34100083 + 59 66 105 2 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34098612-34098807(+) PUM2 PUM2_1 chr21 34098705 34098712 + 93 100 195 2 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_1 chr21 34099722 34099729 + 65 72 170 2 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_1 chr21 34099724 34099731 + 67 74 170 2 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_1 chr21 34099762 34099769 + 105 112 170 2 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105532-34105707(+) PUM2 PUM2_1 chr21 34105602 34105609 + 70 77 175 3 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105532-34105707(+) PUM2 PUM2_1 chr21 34105611 34105618 + 79 86 175 3 3.64646 0.000819 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34788275-34788440(-) PUM2 PUM2_1 chr21 34788433 34788440 - 1 8 165 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34788275-34788440(-) PUM2 PUM2_1 chr21 34788319 34788326 - 115 122 165 1 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_1 chr21 34887732 34887739 - 89 96 195 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_1 chr21 34887705 34887712 - 116 123 195 1 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_1 chr21 34887697 34887704 - 124 131 195 1 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_1 chr21 34887695 34887702 - 126 133 195 1 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34791730-34791905(-) PUM2 PUM2_1 chr21 34791779 34791786 - 120 127 175 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_1 chr21 36375534 36375541 + 307 314 745 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_1 chr21 36375544 36375551 + 317 324 745 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_1 chr21 36375731 36375738 + 504 511 745 1 4.56566 0.00063 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_1 chr21 36375744 36375751 + 517 524 745 1 4.56566 0.00063 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_1 chr21 36375812 36375819 + 585 592 745 1 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_1 chr21 36375845 36375852 + 618 625 745 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36376182-36376512(+) PUM2 PUM2_1 chr21 36376310 36376317 + 128 135 330 1 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36376182-36376512(+) PUM2 PUM2_1 chr21 36376312 36376319 + 130 137 330 1 4.71717 0.000332 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36376182-36376512(+) PUM2 PUM2_1 chr21 36376422 36376429 + 240 247 330 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37202909-37203104(+) PUM2 PUM2_1 chr21 37203027 37203034 + 118 125 195 1 12.9798 4.95e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37223419-37223584(-) PUM2 PUM2_1 chr21 37223515 37223522 - 63 70 165 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37223419-37223584(-) PUM2 PUM2_1 chr21 37223459 37223466 - 119 126 165 1 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37223419-37223584(-) PUM2 PUM2_1 chr21 37223424 37223431 - 154 161 165 1 4.69697 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37223419-37223584(-) PUM2 PUM2_1 chr21 37223420 37223427 - 158 165 165 1 4.56566 0.00063 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37513660-37513945(+) PUM2 PUM2_1 chr21 37513892 37513899 + 232 239 285 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514945-37515225(+) PUM2 PUM2_1 chr21 37515015 37515022 + 70 77 280 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514945-37515225(+) PUM2 PUM2_1 chr21 37515084 37515091 + 139 146 280 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514945-37515225(+) PUM2 PUM2_1 chr21 37515086 37515093 + 141 148 280 1 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514610-37514715(+) PUM2 PUM2_1 chr21 37514674 37514681 + 64 71 105 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38156333-38156511(+) PUM2 PUM2_1 chr21 38156461 38156468 + 128 135 178 1 10.6465 9.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823543-38823783(+) PUM2 PUM2_1 chr21 38823684 38823691 + 141 148 240 1 10.6465 9.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_1 chr21 38823341 38823348 + 68 75 190 1 14.3636 1.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_1 chr21 38823390 38823397 + 117 124 190 1 4.78788 0.000283 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_1 chr21 38823406 38823413 + 133 140 190 1 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_1 chr21 39175562 39175569 - 80 87 200 1 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_1 chr21 39175515 39175522 - 127 134 200 1 8.07071 0.000128 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_1 chr21 39175463 39175470 - 179 186 200 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_1 chr21 41988361 41988368 - 68 75 195 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_1 chr21 41988342 41988349 - 87 94 195 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_1 chr21 41988303 41988310 - 126 133 195 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43760950-43761125(+) PUM2 PUM2_1 chr21 43761044 43761051 + 94 101 175 1 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43982948-43983178(+) PUM2 PUM2_1 chr21 43983059 43983066 + 111 118 230 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44805616-44805856(-) PUM2 PUM2_1 chr21 44805668 44805675 - 182 189 240 1 10.6465 9.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44805616-44805856(-) PUM2 PUM2_1 chr21 44805641 44805648 - 209 216 240 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44805616-44805856(-) PUM2 PUM2_1 chr21 44805634 44805641 - 216 223 240 1 4.54545 0.000789 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44861162-44861271(-) PUM2 PUM2_1 chr21 44861192 44861199 - 73 80 109 1 11.8788 8.1e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:45602615-45602770(+) PUM2 PUM2_1 chr21 45602699 45602706 + 84 91 155 1 12.0303 6.48e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:45602615-45602770(+) PUM2 PUM2_1 chr21 45602733 45602740 + 118 125 155 1 4.87879 0.000191 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46324121-46324226(+) PUM2 PUM2_1 chr21 46324158 46324165 + 37 44 105 1 14.2121 3.34e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569284-46569479(+) PUM2 PUM2_1 chr21 46569301 46569308 + 17 24 195 1 3.40404 0.00091 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569284-46569479(+) PUM2 PUM2_1 chr21 46569382 46569389 + 98 105 195 1 4.63636 0.000578 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569554-46569659(+) PUM2 PUM2_1 chr21 46569594 46569601 + 40 47 105 1 11.8788 8.1e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569554-46569659(+) PUM2 PUM2_1 chr21 46569651 46569658 + 97 104 105 1 5.0303 0.000159 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_2 chr21 14371383 14371390 - 50 57 325 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_2 chr21 14371187 14371194 - 246 253 325 1 -3.17172 0.000497 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_2 chr21 14485768 14485775 - 113 120 295 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961188-14961428(-) PUM2 PUM2_2 chr21 14961325 14961332 - 97 104 240 2 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961188-14961428(-) PUM2 PUM2_2 chr21 14961274 14961281 - 148 155 240 2 -3.24242 0.000754 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_2 chr21 14961712 14961719 - 340 347 405 2 6.40404 0.0001 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_2 chr21 14961666 14961673 - 386 393 405 2 6.40404 0.0001 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_2 chr21 14961712 14961719 - 341 348 405 2 6.40404 0.0001 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_2 chr21 14961666 14961673 - 387 394 405 2 6.40404 0.0001 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961234-14961429(-) PUM2 PUM2_2 chr21 14961325 14961332 - 98 105 195 2 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961234-14961429(-) PUM2 PUM2_2 chr21 14961274 14961281 - 149 156 195 2 -3.24242 0.000754 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:28928288-28928403(-) PUM2 PUM2_2 chr21 28928377 28928384 - 20 27 115 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29326058-29326273(+) PUM2 PUM2_2 chr21 29326166 29326173 + 108 115 215 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29326058-29326273(+) PUM2 PUM2_2 chr21 29326260 29326267 + 202 209 215 1 -3.24242 0.000754 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32628758-32628913(-) PUM2 PUM2_2 chr21 32628809 32628816 - 98 105 155 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_2 chr21 33437400 33437407 + 163 170 284 1 15.9798 1.5e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33504080-33504270(-) PUM2 PUM2_2 chr21 33504165 33504172 - 99 106 190 1 6.31313 0.000284 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_2 chr21 33576612 33576619 + 98 105 330 1 -3.24242 0.000754 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105529-34105709(+) PUM2 PUM2_2 chr21 34105530 34105537 + 1 8 180 1 -3.17172 0.000497 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105529-34105709(+) PUM2 PUM2_2 chr21 34105611 34105618 + 82 89 180 3 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_2 chr21 34099702 34099709 + 42 49 165 2 6.31313 0.000284 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105530-34105710(+) PUM2 PUM2_2 chr21 34105611 34105618 + 81 88 180 3 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_2 chr21 34099702 34099709 + 45 52 170 2 6.31313 0.000284 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105532-34105707(+) PUM2 PUM2_2 chr21 34105611 34105618 + 79 86 175 3 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_2 chr21 36375341 36375348 + 114 121 745 1 6.31313 0.000284 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37202909-37203104(+) PUM2 PUM2_2 chr21 37203027 37203034 + 118 125 195 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37513660-37513945(+) PUM2 PUM2_2 chr21 37513708 37513715 + 48 55 285 1 6.40404 0.0001 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38156333-38156511(+) PUM2 PUM2_2 chr21 38156461 38156468 + 128 135 178 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823543-38823783(+) PUM2 PUM2_2 chr21 38823684 38823691 + 141 148 240 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43982948-43983178(+) PUM2 PUM2_2 chr21 43983067 43983074 + 119 126 230 1 6.31313 0.000284 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44805616-44805856(-) PUM2 PUM2_2 chr21 44805847 44805854 - 3 10 240 1 -3.17172 0.000497 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44805616-44805856(-) PUM2 PUM2_2 chr21 44805668 44805675 - 182 189 240 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:45602615-45602770(+) PUM2 PUM2_2 chr21 45602708 45602715 + 93 100 155 1 6.31313 0.000284 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569554-46569659(+) PUM2 PUM2_2 chr21 46569651 46569658 + 97 104 105 1 6.30303 0.000377 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:5240799-5240909(-) PUM2 PUM2_3 chr21 5240861 5240868 - 42 49 110 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_3 chr21 14371143 14371150 - 290 297 325 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_3 chr21 14485810 14485817 - 71 78 295 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_3 chr21 14485768 14485775 - 113 120 295 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_3 chr21 14485730 14485737 - 151 158 295 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_3 chr21 14485692 14485699 - 189 196 295 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485227-14485462(-) PUM2 PUM2_3 chr21 14485285 14485292 - 171 178 235 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485227-14485462(-) PUM2 PUM2_3 chr21 14485254 14485261 - 202 209 235 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962128-14962318(-) PUM2 PUM2_3 chr21 14962220 14962227 - 92 99 190 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961188-14961428(-) PUM2 PUM2_3 chr21 14961325 14961332 - 97 104 240 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_3 chr21 14962005 14962012 - 47 54 405 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_3 chr21 14961945 14961952 - 107 114 405 2 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_3 chr21 14961842 14961849 - 210 217 405 2 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_3 chr21 14962005 14962012 - 48 55 405 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_3 chr21 14961945 14961952 - 108 115 405 2 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_3 chr21 14961842 14961849 - 211 218 405 2 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961234-14961429(-) PUM2 PUM2_3 chr21 14961325 14961332 - 98 105 195 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962129-14962314(-) PUM2 PUM2_3 chr21 14962220 14962227 - 88 95 185 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788950-17789135(-) PUM2 PUM2_3 chr21 17789024 17789031 - 105 112 185 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788966-17789136(-) PUM2 PUM2_3 chr21 17789024 17789031 - 106 113 170 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:28928288-28928403(-) PUM2 PUM2_3 chr21 28928377 28928384 - 20 27 115 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29345713-29345908(+) PUM2 PUM2_3 chr21 29345791 29345798 + 78 85 195 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29326058-29326273(+) PUM2 PUM2_3 chr21 29326166 29326173 + 108 115 215 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:31668760-31668905(+) PUM2 PUM2_3 chr21 31668867 31668874 + 107 114 145 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:31671207-31671477(-) PUM2 PUM2_3 chr21 31671211 31671218 - 260 267 270 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32628758-32628913(-) PUM2 PUM2_3 chr21 32628809 32628816 - 98 105 155 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_3 chr21 32734896 32734903 - 121 128 500 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_3 chr21 32734887 32734894 - 130 137 500 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_3 chr21 32734647 32734654 - 370 377 500 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_3 chr21 32734638 32734645 - 379 386 500 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32733913-32734158(-) PUM2 PUM2_3 chr21 32734041 32734048 - 111 118 245 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32733913-32734158(-) PUM2 PUM2_3 chr21 32733935 32733942 - 217 224 245 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_3 chr21 33437428 33437435 + 191 198 284 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_3 chr21 33437440 33437447 + 203 210 284 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_3 chr21 33437481 33437488 + 244 251 284 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33450581-33450681(-) PUM2 PUM2_3 chr21 33450630 33450637 - 45 52 100 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33450581-33450681(-) PUM2 PUM2_3 chr21 33450622 33450629 - 53 60 100 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_3 chr21 33576643 33576650 + 129 136 330 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_3 chr21 33576671 33576678 + 157 164 330 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_3 chr21 33576685 33576692 + 171 178 330 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_3 chr21 33560567 33560574 + 66 73 166 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_3 chr21 33560577 33560584 + 76 83 166 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34098610-34098805(+) PUM2 PUM2_3 chr21 34098705 34098712 + 95 102 195 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_3 chr21 34099724 34099731 + 64 71 165 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_3 chr21 34099762 34099769 + 102 109 165 2 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34142892-34143034(+) PUM2 PUM2_3 chr21 34142958 34142965 + 66 73 142 2 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34142890-34143080(+) PUM2 PUM2_3 chr21 34142958 34142965 + 68 75 190 2 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34098612-34098807(+) PUM2 PUM2_3 chr21 34098705 34098712 + 93 100 195 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_3 chr21 34099724 34099731 + 67 74 170 2 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_3 chr21 34099762 34099769 + 105 112 170 2 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34788275-34788440(-) PUM2 PUM2_3 chr21 34788433 34788440 - 1 8 165 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_3 chr21 34887732 34887739 - 89 96 195 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_3 chr21 34887705 34887712 - 116 123 195 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34791730-34791905(-) PUM2 PUM2_3 chr21 34791779 34791786 - 120 127 175 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_3 chr21 36375534 36375541 + 307 314 745 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_3 chr21 36375544 36375551 + 317 324 745 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_3 chr21 36375731 36375738 + 504 511 745 1 6.13131 0.000264 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_3 chr21 36375744 36375751 + 517 524 745 1 6.13131 0.000264 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_3 chr21 36375845 36375852 + 618 625 745 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36376182-36376512(+) PUM2 PUM2_3 chr21 36376310 36376317 + 128 135 330 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37202909-37203104(+) PUM2 PUM2_3 chr21 37203027 37203034 + 118 125 195 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37223419-37223584(-) PUM2 PUM2_3 chr21 37223515 37223522 - 63 70 165 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37223419-37223584(-) PUM2 PUM2_3 chr21 37223420 37223427 - 158 165 165 1 6.13131 0.000264 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37513660-37513945(+) PUM2 PUM2_3 chr21 37513892 37513899 + 232 239 285 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514945-37515225(+) PUM2 PUM2_3 chr21 37515015 37515022 + 70 77 280 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514610-37514715(+) PUM2 PUM2_3 chr21 37514674 37514681 + 64 71 105 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_3 chr21 38823341 38823348 + 68 75 190 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_3 chr21 39175463 39175470 - 179 186 200 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_3 chr21 41988361 41988368 - 68 75 195 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_3 chr21 41988342 41988349 - 87 94 195 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_3 chr21 41988303 41988310 - 126 133 195 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43982948-43983178(+) PUM2 PUM2_3 chr21 43983059 43983066 + 111 118 230 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44805616-44805856(-) PUM2 PUM2_3 chr21 44805641 44805648 - 209 216 240 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44805616-44805856(-) PUM2 PUM2_3 chr21 44805634 44805641 - 216 223 240 1 6.11111 0.000423 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44861162-44861271(-) PUM2 PUM2_3 chr21 44861192 44861199 - 73 80 109 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:45602615-45602770(+) PUM2 PUM2_3 chr21 45602733 45602740 + 118 125 155 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46324121-46324226(+) PUM2 PUM2_3 chr21 46324158 46324165 + 37 44 105 1 15.7778 1.72e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569284-46569479(+) PUM2 PUM2_3 chr21 46569382 46569389 + 98 105 195 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569554-46569659(+) PUM2 PUM2_3 chr21 46569594 46569601 + 40 47 105 1 6.20202 0.000212 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:5240799-5240909(-) PUM2 PUM2_4 chr21 5240861 5240868 - 42 49 110 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_4 chr21 14371143 14371150 - 290 297 325 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_4 chr21 14485810 14485817 - 71 78 295 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_4 chr21 14485768 14485775 - 113 120 295 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485227-14485462(-) PUM2 PUM2_4 chr21 14485393 14485400 - 63 70 235 1 -3.30303 0.0008 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485227-14485462(-) PUM2 PUM2_4 chr21 14485285 14485292 - 171 178 235 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962128-14962318(-) PUM2 PUM2_4 chr21 14962220 14962227 - 92 99 190 2 15.8485 1.64e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962128-14962318(-) PUM2 PUM2_4 chr21 14962178 14962185 - 134 141 190 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961188-14961428(-) PUM2 PUM2_4 chr21 14961325 14961332 - 97 104 240 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_4 chr21 14962005 14962012 - 47 54 405 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_4 chr21 14961945 14961952 - 107 114 405 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_4 chr21 14961842 14961849 - 210 217 405 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_4 chr21 14962005 14962012 - 48 55 405 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_4 chr21 14961945 14961952 - 108 115 405 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_4 chr21 14961842 14961849 - 211 218 405 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961234-14961429(-) PUM2 PUM2_4 chr21 14961325 14961332 - 98 105 195 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962129-14962314(-) PUM2 PUM2_4 chr21 14962220 14962227 - 88 95 185 2 15.8485 1.64e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962129-14962314(-) PUM2 PUM2_4 chr21 14962178 14962185 - 130 137 185 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788950-17789135(-) PUM2 PUM2_4 chr21 17789024 17789031 - 105 112 185 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788966-17789136(-) PUM2 PUM2_4 chr21 17789024 17789031 - 106 113 170 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:28928288-28928403(-) PUM2 PUM2_4 chr21 28928377 28928384 - 20 27 115 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:28928288-28928403(-) PUM2 PUM2_4 chr21 28928347 28928354 - 50 57 115 1 -3.30303 0.0008 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29345713-29345908(+) PUM2 PUM2_4 chr21 29345791 29345798 + 78 85 195 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29326058-29326273(+) PUM2 PUM2_4 chr21 29326130 29326137 + 72 79 215 1 -3.30303 0.0008 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29326058-29326273(+) PUM2 PUM2_4 chr21 29326166 29326173 + 108 115 215 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32628758-32628913(-) PUM2 PUM2_4 chr21 32628809 32628816 - 98 105 155 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_4 chr21 32734887 32734894 - 130 137 500 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32733913-32734158(-) PUM2 PUM2_4 chr21 32734041 32734048 - 111 118 245 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_4 chr21 33437440 33437447 + 203 210 284 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33450581-33450681(-) PUM2 PUM2_4 chr21 33450622 33450629 - 53 60 100 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33524008-33524183(-) PUM2 PUM2_4 chr21 33524055 33524062 - 122 129 175 1 -3.30303 0.0008 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_4 chr21 33576568 33576575 + 54 61 330 1 6.18182 0.000406 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_4 chr21 33576643 33576650 + 129 136 330 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_4 chr21 33560567 33560574 + 66 73 166 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_4 chr21 33560577 33560584 + 76 83 166 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33577980-33578190(-) PUM2 PUM2_4 chr21 33578135 33578142 - 49 56 210 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_4 chr21 34099724 34099731 + 64 71 165 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_4 chr21 34099762 34099769 + 102 109 165 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_4 chr21 34099724 34099731 + 67 74 170 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_4 chr21 34099762 34099769 + 105 112 170 2 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_4 chr21 34887732 34887739 - 89 96 195 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_4 chr21 34887705 34887712 - 116 123 195 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_4 chr21 36375230 36375237 + 3 10 745 1 -3.30303 0.0008 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_4 chr21 36375236 36375243 + 9 16 745 1 -3.30303 0.0008 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_4 chr21 36375374 36375381 + 147 154 745 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_4 chr21 36375534 36375541 + 307 314 745 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36376182-36376512(+) PUM2 PUM2_4 chr21 36376310 36376317 + 128 135 330 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37202909-37203104(+) PUM2 PUM2_4 chr21 37203027 37203034 + 118 125 195 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514610-37514715(+) PUM2 PUM2_4 chr21 37514693 37514700 + 83 90 105 1 -3.30303 0.0008 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_4 chr21 38823341 38823348 + 68 75 190 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_4 chr21 39175515 39175522 - 127 134 200 1 6.27273 0.000156 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_4 chr21 39175449 39175456 - 193 200 200 1 -3.30303 0.0008 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_4 chr21 41988373 41988380 - 56 63 195 1 6.18182 0.000406 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_4 chr21 41988361 41988368 - 68 75 195 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_4 chr21 41988324 41988331 - 105 112 195 1 6.18182 0.000406 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43982948-43983178(+) PUM2 PUM2_4 chr21 43983059 43983066 + 111 118 230 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46324121-46324226(+) PUM2 PUM2_4 chr21 46324158 46324165 + 37 44 105 1 6.20202 0.000255 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:5240799-5240909(-) PUM2 PUM2_5 chr21 5240861 5240870 - 40 49 110 1 13.7677 4.96e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_5 chr21 14371383 14371392 - 48 57 325 1 11.4646 6.71e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_5 chr21 14371231 14371240 - 200 209 325 1 7.60606 0.000682 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_5 chr21 14371201 14371210 - 230 239 325 1 8.43434 0.000461 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_5 chr21 14371170 14371179 - 261 270 325 1 8.27273 0.000508 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14371114-14371439(-) PUM2 PUM2_5 chr21 14371143 14371152 - 288 297 325 1 11.9293 4.81e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_5 chr21 14485810 14485819 - 69 78 295 1 13.7677 4.96e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_5 chr21 14485768 14485777 - 111 120 295 1 13.2727 8.98e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485592-14485887(-) PUM2 PUM2_5 chr21 14485719 14485728 - 160 169 295 1 8.47475 0.000457 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14485227-14485462(-) PUM2 PUM2_5 chr21 14485285 14485294 - 169 178 235 1 11.1212 8.74e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962128-14962318(-) PUM2 PUM2_5 chr21 14962220 14962229 - 90 99 190 2 10.0909 0.00019 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961188-14961428(-) PUM2 PUM2_5 chr21 14961325 14961334 - 95 104 240 2 11.6566 6.11e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962045 14962054 - 5 14 405 2 7.66667 0.000664 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962038 14962047 - 12 21 405 2 8.90909 0.00037 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962036 14962045 - 14 23 405 2 11.0303 9.55e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962034 14962043 - 16 25 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962032 14962041 - 18 27 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962030 14962039 - 20 29 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962028 14962037 - 22 31 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962026 14962035 - 24 33 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962024 14962033 - 26 35 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962022 14962031 - 28 37 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962020 14962029 - 30 39 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962018 14962027 - 32 41 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962016 14962025 - 34 43 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962014 14962023 - 36 45 405 2 6.91919 0.000926 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962005 14962014 - 45 54 405 2 13.9192 3.92e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962003 14962012 - 47 56 405 2 9.43434 0.00027 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14962001 14962010 - 49 58 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961999 14962008 - 51 60 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961997 14962006 - 53 62 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961995 14962004 - 55 64 405 2 9.52525 0.000262 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961945 14961954 - 105 114 405 2 10.8384 0.000118 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961908 14961917 - 142 151 405 2 8.29293 0.000501 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961861 14961870 - 189 198 405 2 10.5455 0.000137 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961850 14961859 - 200 209 405 2 7.50505 0.000711 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961842 14961851 - 208 217 405 2 11.1212 8.74e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961777 14961786 - 273 282 405 2 10.8384 0.000118 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961653-14962058(-) PUM2 PUM2_5 chr21 14961704 14961713 - 346 355 405 2 7.15152 0.000846 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962045 14962054 - 6 15 405 2 7.66667 0.000664 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962038 14962047 - 13 22 405 2 8.90909 0.00037 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962036 14962045 - 15 24 405 2 11.0303 9.55e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962034 14962043 - 17 26 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962032 14962041 - 19 28 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962030 14962039 - 21 30 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962028 14962037 - 23 32 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962026 14962035 - 25 34 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962024 14962033 - 27 36 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962022 14962031 - 29 38 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962020 14962029 - 31 40 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962018 14962027 - 33 42 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962016 14962025 - 35 44 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962014 14962023 - 37 46 405 2 6.91919 0.000926 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962005 14962014 - 46 55 405 2 13.9192 3.92e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962003 14962012 - 48 57 405 2 9.43434 0.00027 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14962001 14962010 - 50 59 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961999 14962008 - 52 61 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961997 14962006 - 54 63 405 2 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961995 14962004 - 56 65 405 2 9.52525 0.000262 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961945 14961954 - 106 115 405 2 10.8384 0.000118 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961908 14961917 - 143 152 405 2 8.29293 0.000501 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961861 14961870 - 190 199 405 2 10.5455 0.000137 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961850 14961859 - 201 210 405 2 7.50505 0.000711 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961842 14961851 - 209 218 405 2 11.1212 8.74e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961777 14961786 - 274 283 405 2 10.8384 0.000118 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961654-14962059(-) PUM2 PUM2_5 chr21 14961704 14961713 - 347 356 405 2 7.15152 0.000846 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14961234-14961429(-) PUM2 PUM2_5 chr21 14961325 14961334 - 96 105 195 2 11.6566 6.11e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:14962129-14962314(-) PUM2 PUM2_5 chr21 14962220 14962229 - 86 95 185 2 10.0909 0.00019 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788950-17789135(-) PUM2 PUM2_5 chr21 17789055 17789064 - 72 81 185 2 8.12121 0.000548 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788950-17789135(-) PUM2 PUM2_5 chr21 17789053 17789062 - 74 83 185 2 10.3131 0.00016 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788950-17789135(-) PUM2 PUM2_5 chr21 17789024 17789033 - 103 112 185 2 12.0404 4.11e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788950-17789135(-) PUM2 PUM2_5 chr21 17789022 17789031 - 105 114 185 2 7.45455 0.000727 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788966-17789136(-) PUM2 PUM2_5 chr21 17789055 17789064 - 73 82 170 2 8.12121 0.000548 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788966-17789136(-) PUM2 PUM2_5 chr21 17789053 17789062 - 75 84 170 2 10.3131 0.00016 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788966-17789136(-) PUM2 PUM2_5 chr21 17789024 17789033 - 104 113 170 2 12.0404 4.11e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:17788966-17789136(-) PUM2 PUM2_5 chr21 17789022 17789031 - 106 115 170 2 7.45455 0.000727 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:28928288-28928403(-) PUM2 PUM2_5 chr21 28928377 28928386 - 18 27 115 1 13.5354 7.95e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29345143-29345258(+) PUM2 PUM2_5 chr21 29345207 29345216 + 64 73 115 1 12.3737 2.89e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29345713-29345908(+) PUM2 PUM2_5 chr21 29345789 29345798 + 76 85 195 1 12.1515 3.69e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:29326058-29326273(+) PUM2 PUM2_5 chr21 29326164 29326173 + 106 115 215 1 11.6768 6.01e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:31668760-31668905(+) PUM2 PUM2_5 chr21 31668798 31668807 + 38 47 145 1 6.87879 0.000939 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:31671207-31671477(-) PUM2 PUM2_5 chr21 31671335 31671344 - 134 143 270 1 8.55556 0.000433 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32628758-32628913(-) PUM2 PUM2_5 chr21 32628809 32628818 - 96 105 155 1 12.7071 2.2e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_5 chr21 32734896 32734905 - 119 128 500 1 11.4545 6.81e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_5 chr21 32734887 32734896 - 128 137 500 1 14.7071 9.81e-07 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_5 chr21 32734885 32734894 - 130 139 500 1 7.45455 0.000727 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_5 chr21 32734879 32734888 - 136 145 500 1 10.2323 0.000167 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_5 chr21 32734862 32734871 - 153 162 500 1 7.77778 0.00064 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_5 chr21 32734647 32734656 - 368 377 500 1 10.404 0.000149 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_5 chr21 32734638 32734647 - 377 386 500 1 8.50505 0.000445 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_5 chr21 32734626 32734635 - 389 398 500 1 8.41414 0.000465 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32734523-32735023(-) PUM2 PUM2_5 chr21 32734624 32734633 - 391 400 500 1 9.52525 0.000262 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32733913-32734158(-) PUM2 PUM2_5 chr21 32734041 32734050 - 109 118 245 1 12.7172 2.11e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32733913-32734158(-) PUM2 PUM2_5 chr21 32733941 32733950 - 209 218 245 1 8.0 0.000585 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:32733913-32734158(-) PUM2 PUM2_5 chr21 32733935 32733944 - 215 224 245 1 9.31313 0.00029 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_5 chr21 33437398 33437407 + 161 170 284 1 8.80808 0.000397 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_5 chr21 33437426 33437435 + 189 198 284 1 8.26263 0.000513 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_5 chr21 33437438 33437447 + 201 210 284 1 11.9394 4.69e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33437237-33437521(+) PUM2 PUM2_5 chr21 33437493 33437502 + 256 265 284 1 10.9091 0.000109 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33450581-33450681(-) PUM2 PUM2_5 chr21 33450622 33450631 - 51 60 100 1 13.9192 3.92e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33504080-33504270(-) PUM2 PUM2_5 chr21 33504165 33504174 - 97 106 190 1 6.72727 0.000983 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33524008-33524183(-) PUM2 PUM2_5 chr21 33524156 33524165 - 19 28 175 1 9.38384 0.000279 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33524008-33524183(-) PUM2 PUM2_5 chr21 33524135 33524144 - 40 49 175 1 8.35354 0.000481 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33524008-33524183(-) PUM2 PUM2_5 chr21 33524083 33524092 - 92 101 175 1 8.48485 0.000453 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33524008-33524183(-) PUM2 PUM2_5 chr21 33524047 33524056 - 128 137 175 1 10.9293 0.000107 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33524008-33524183(-) PUM2 PUM2_5 chr21 33524030 33524039 - 145 154 175 1 8.61616 0.000424 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_5 chr21 33576641 33576650 + 127 136 330 1 11.6263 6.33e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_5 chr21 33576669 33576678 + 155 164 330 1 9.56566 0.000256 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_5 chr21 33576683 33576692 + 169 178 330 1 9.54545 0.00026 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_5 chr21 33576725 33576734 + 211 220 330 1 9.9899 0.000199 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33576514-33576844(+) PUM2 PUM2_5 chr21 33576754 33576763 + 240 249 330 1 7.64646 0.000672 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33558740-33558910(+) PUM2 PUM2_5 chr21 33558832 33558841 + 92 101 170 1 7.71717 0.000655 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33558740-33558910(+) PUM2 PUM2_5 chr21 33558869 33558878 + 129 138 170 1 7.56566 0.000695 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33558740-33558910(+) PUM2 PUM2_5 chr21 33558892 33558901 + 152 161 170 1 10.1111 0.000186 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_5 chr21 33560565 33560574 + 64 73 166 1 12.0404 4.11e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_5 chr21 33560567 33560576 + 66 75 166 1 9.43434 0.00027 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_5 chr21 33560569 33560578 + 68 77 166 1 8.26263 0.000513 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_5 chr21 33560575 33560584 + 74 83 166 1 12.9798 1.4e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_5 chr21 33560581 33560590 + 80 89 166 1 9.19192 0.000314 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_5 chr21 33560583 33560592 + 82 91 166 1 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_5 chr21 33560585 33560594 + 84 93 166 1 10.2424 0.000165 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33560501-33560667(+) PUM2 PUM2_5 chr21 33560587 33560596 + 86 95 166 1 7.34343 0.000766 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:33577980-33578190(-) PUM2 PUM2_5 chr21 33578071 33578080 - 111 120 210 1 12.9394 1.5e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105529-34105709(+) PUM2 PUM2_5 chr21 34105600 34105609 + 71 80 180 3 10.2525 0.000164 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105529-34105709(+) PUM2 PUM2_5 chr21 34105609 34105618 + 80 89 180 3 10.7475 0.000121 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105529-34105709(+) PUM2 PUM2_5 chr21 34105653 34105662 + 124 133 180 3 7.06061 0.000878 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34098610-34098805(+) PUM2 PUM2_5 chr21 34098703 34098712 + 93 102 195 2 8.50505 0.000445 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_5 chr21 34099720 34099729 + 60 69 165 2 8.27273 0.000508 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_5 chr21 34099722 34099731 + 62 71 165 2 13.1111 1.1e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099660-34099825(+) PUM2 PUM2_5 chr21 34099760 34099769 + 100 109 165 2 12.1515 3.69e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105530-34105710(+) PUM2 PUM2_5 chr21 34105600 34105609 + 70 79 180 3 10.2525 0.000164 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105530-34105710(+) PUM2 PUM2_5 chr21 34105609 34105618 + 79 88 180 3 10.7475 0.000121 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105530-34105710(+) PUM2 PUM2_5 chr21 34105653 34105662 + 123 132 180 3 7.06061 0.000878 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100020-34100120(+) PUM2 PUM2_5 chr21 34100072 34100081 + 52 61 100 2 7.25253 0.000803 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100020-34100120(+) PUM2 PUM2_5 chr21 34100074 34100083 + 54 63 100 2 12.3939 2.8e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100020-34100120(+) PUM2 PUM2_5 chr21 34100082 34100091 + 62 71 100 2 9.24242 0.000306 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100017-34100122(+) PUM2 PUM2_5 chr21 34100072 34100081 + 55 64 105 2 7.25253 0.000803 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100017-34100122(+) PUM2 PUM2_5 chr21 34100074 34100083 + 57 66 105 2 12.3939 2.8e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34100017-34100122(+) PUM2 PUM2_5 chr21 34100082 34100091 + 65 74 105 2 9.24242 0.000306 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34098612-34098807(+) PUM2 PUM2_5 chr21 34098703 34098712 + 91 100 195 2 8.50505 0.000445 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_5 chr21 34099720 34099729 + 63 72 170 2 8.27273 0.000508 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_5 chr21 34099722 34099731 + 65 74 170 2 13.1111 1.1e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34099657-34099827(+) PUM2 PUM2_5 chr21 34099760 34099769 + 103 112 170 2 12.1515 3.69e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105532-34105707(+) PUM2 PUM2_5 chr21 34105600 34105609 + 68 77 175 3 10.2525 0.000164 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105532-34105707(+) PUM2 PUM2_5 chr21 34105609 34105618 + 77 86 175 3 10.7475 0.000121 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34105532-34105707(+) PUM2 PUM2_5 chr21 34105653 34105662 + 121 130 175 3 7.06061 0.000878 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34788275-34788440(-) PUM2 PUM2_5 chr21 34788319 34788328 - 113 122 165 1 9.17172 0.00032 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_5 chr21 34887755 34887764 - 64 73 195 1 6.70707 0.000993 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_5 chr21 34887737 34887746 - 82 91 195 1 7.24242 0.000807 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_5 chr21 34887732 34887741 - 87 96 195 1 12.7172 2.11e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_5 chr21 34887705 34887714 - 114 123 195 1 13.9192 3.92e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_5 chr21 34887703 34887712 - 116 125 195 1 8.71717 0.000411 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_5 chr21 34887697 34887706 - 122 131 195 1 9.17172 0.00032 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:34887632-34887827(-) PUM2 PUM2_5 chr21 34887695 34887704 - 124 133 195 1 11.0303 9.55e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_5 chr21 36375339 36375348 + 112 121 745 1 7.25253 0.000803 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_5 chr21 36375372 36375381 + 145 154 745 1 7.20202 0.00083 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_5 chr21 36375532 36375541 + 305 314 745 1 11.9293 4.81e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_5 chr21 36375542 36375551 + 315 324 745 1 10.101 0.000188 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_5 chr21 36375655 36375664 + 428 437 745 1 7.67677 0.000661 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_5 chr21 36375742 36375751 + 515 524 745 1 9.0202 0.000355 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_5 chr21 36375810 36375819 + 583 592 745 1 12.101 3.79e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_5 chr21 36375812 36375821 + 585 594 745 1 7.77778 0.00064 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36375227-36375972(+) PUM2 PUM2_5 chr21 36375929 36375938 + 702 711 745 1 7.92929 0.000611 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36376182-36376512(+) PUM2 PUM2_5 chr21 36376308 36376317 + 126 135 330 1 13.9192 3.92e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36376182-36376512(+) PUM2 PUM2_5 chr21 36376310 36376319 + 128 137 330 1 9.43434 0.00027 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36376182-36376512(+) PUM2 PUM2_5 chr21 36376343 36376352 + 161 170 330 1 6.92929 0.000923 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:36376182-36376512(+) PUM2 PUM2_5 chr21 36376469 36376478 + 287 296 330 1 9.29293 0.000294 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37202909-37203104(+) PUM2 PUM2_5 chr21 37203025 37203034 + 116 125 195 1 14.3232 1.95e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37223419-37223584(-) PUM2 PUM2_5 chr21 37223459 37223468 - 117 126 165 1 11.0606 9.24e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37223419-37223584(-) PUM2 PUM2_5 chr21 37223447 37223456 - 129 138 165 1 8.59596 0.000428 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37223419-37223584(-) PUM2 PUM2_5 chr21 37223420 37223429 - 156 165 165 1 7.16162 0.000846 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37513660-37513945(+) PUM2 PUM2_5 chr21 37513905 37513914 + 245 254 285 1 7.0404 0.000882 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514945-37515225(+) PUM2 PUM2_5 chr21 37515006 37515015 + 61 70 280 1 7.15152 0.000846 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514945-37515225(+) PUM2 PUM2_5 chr21 37515084 37515093 + 139 148 280 1 12.3939 2.8e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514945-37515225(+) PUM2 PUM2_5 chr21 37515122 37515131 + 177 186 280 1 7.71717 0.000655 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514610-37514715(+) PUM2 PUM2_5 chr21 37514620 37514629 + 10 19 105 1 7.35354 0.00076 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:37514610-37514715(+) PUM2 PUM2_5 chr21 37514672 37514681 + 62 71 105 1 10.101 0.000188 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38156333-38156511(+) PUM2 PUM2_5 chr21 38156459 38156468 + 126 135 178 1 11.7677 5.5e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823543-38823783(+) PUM2 PUM2_5 chr21 38823550 38823559 + 7 16 240 1 6.92929 0.000923 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823543-38823783(+) PUM2 PUM2_5 chr21 38823557 38823566 + 14 23 240 1 8.07071 0.000563 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823543-38823783(+) PUM2 PUM2_5 chr21 38823682 38823691 + 139 148 240 1 13.6061 6.92e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823543-38823783(+) PUM2 PUM2_5 chr21 38823760 38823769 + 217 226 240 1 9.9697 0.000204 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_5 chr21 38823339 38823348 + 66 75 190 1 14.7071 9.81e-07 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_5 chr21 38823341 38823350 + 68 77 190 1 8.71717 0.000411 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_5 chr21 38823388 38823397 + 115 124 190 1 8.89899 0.000373 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_5 chr21 38823404 38823413 + 131 140 190 1 12.9394 1.5e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:38823273-38823463(+) PUM2 PUM2_5 chr21 38823411 38823420 + 138 147 190 1 8.33333 0.00049 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_5 chr21 39175591 39175600 - 49 58 200 1 8.66667 0.000419 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_5 chr21 39175562 39175571 - 78 87 200 1 11.3434 7.4e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_5 chr21 39175515 39175524 - 125 134 200 1 10.1616 0.000175 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:39175448-39175648(-) PUM2 PUM2_5 chr21 39175463 39175472 - 177 186 200 1 10.1111 0.000186 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_5 chr21 41988361 41988370 - 66 75 195 1 11.1515 8.53e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_5 chr21 41988342 41988351 - 85 94 195 1 9.05051 0.000345 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:41988240-41988435(-) PUM2 PUM2_5 chr21 41988257 41988266 - 170 179 195 1 8.60606 0.000427 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43693279-43693514(+) PUM2 PUM2_5 chr21 43693399 43693408 + 120 129 235 1 7.35354 0.00076 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43693279-43693514(+) PUM2 PUM2_5 chr21 43693415 43693424 + 136 145 235 1 12.2929 3.08e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43760950-43761125(+) PUM2 PUM2_5 chr21 43761042 43761051 + 92 101 175 1 12.1515 3.69e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:43982948-43983178(+) PUM2 PUM2_5 chr21 43983057 43983066 + 109 118 230 1 12.1717 3.39e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44805616-44805856(-) PUM2 PUM2_5 chr21 44805799 44805808 - 49 58 240 1 6.82828 0.000958 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44805616-44805856(-) PUM2 PUM2_5 chr21 44805668 44805677 - 180 189 240 1 13.6061 6.92e-06 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:44861162-44861271(-) PUM2 PUM2_5 chr21 44861192 44861201 - 71 80 109 1 13.0505 1.29e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:45512427-45512547(+) PUM2 PUM2_5 chr21 45512511 45512520 + 84 93 120 1 8.51515 0.000442 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:45602615-45602770(+) PUM2 PUM2_5 chr21 45602619 45602628 + 4 13 155 1 7.25253 0.000803 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:45602615-45602770(+) PUM2 PUM2_5 chr21 45602697 45602706 + 82 91 155 1 12.1515 3.69e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:45602615-45602770(+) PUM2 PUM2_5 chr21 45602706 45602715 + 91 100 155 1 7.77778 0.00064 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:45602615-45602770(+) PUM2 PUM2_5 chr21 45602731 45602740 + 116 125 155 1 10.1717 0.000174 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46324121-46324226(+) PUM2 PUM2_5 chr21 46324156 46324165 + 35 44 105 1 11.1212 8.74e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569284-46569479(+) PUM2 PUM2_5 chr21 46569299 46569308 + 15 24 195 1 6.81818 0.00096 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569284-46569479(+) PUM2 PUM2_5 chr21 46569388 46569397 + 104 113 195 1 11.5051 6.62e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569554-46569659(+) PUM2 PUM2_5 chr21 46569555 46569564 + 1 10 105 1 9.0101 0.000356 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569554-46569659(+) PUM2 PUM2_5 chr21 46569592 46569601 + 38 47 105 1 11.2222 8.1e-05 - - -sbAn7Po +k562_eclip dewseq_w100_s5 run_id human_v0.1 chr21:46569554-46569659(+) PUM2 PUM2_5 chr21 46569649 46569658 + 95 104 105 1 10.1919 0.000172 - - -sbAn7Po
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.rbpbench_search.slbp_user.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,2 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +data_id method_id run_id user chr1:50-113(+) SLBP_USER RF00032 chr1 89 113 + 39 63 63 1 - - 27.8 1.5e-08 RuDIjV1k
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.rbpbench_search.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,6 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM1 PUM1_3 chr1 24 31 + 14 21 70 1 12.8182 4.87e-05 - - h2FelLqa +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_1 chr1 24 31 + 14 21 70 1 10.404 0.000113 - - HcD7_nJz +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_3 chr1 24 31 + 14 21 70 1 6.20202 0.000212 - - HcD7_nJz +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_4 chr1 24 31 + 14 21 70 1 15.8485 1.64e-05 - - HcD7_nJz +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_5 chr1 22 31 + 12 21 70 1 10.8788 0.000113 - - HcD7_nJz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.table_test.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,6 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +did1 mid1 run_id human_v0.1 chr1:10-80(+) PUM1 PUM1_3 chr1 24 31 + 14 21 70 1 12.8182 4.87e-05 - - NInGOqIN +did2 mid2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_1 chr1 24 31 + 14 21 70 1 10.404 0.000113 - - u7eY1SoG +did2 mid2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_3 chr1 24 31 + 14 21 70 1 6.20202 0.000212 - - u7eY1SoG +did2 mid2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_4 chr1 24 31 + 14 21 70 1 15.8485 1.64e-05 - - u7eY1SoG +did2 mid2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_5 chr1 22 31 + 12 21 70 1 10.8788 0.000113 - - u7eY1SoG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.test_batch.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,6 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +data-id1 method-id1 run_id human_v0.1 chr1:10-80(+) PUM1 PUM1_3 chr1 24 31 + 14 21 70 1 12.8182 4.87e-05 - - TT41sPJM +data-id2 method-id2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_1 chr1 24 31 + 14 21 70 1 10.404 0.000113 - - -dJ6C0OI +data-id2 method-id2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_3 chr1 24 31 + 14 21 70 1 6.20202 0.000212 - - -dJ6C0OI +data-id2 method-id2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_4 chr1 24 31 + 14 21 70 1 15.8485 1.64e-05 - - -dJ6C0OI +data-id2 method-id2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_5 chr1 22 31 + 12 21 70 1 10.8788 0.000113 - - -dJ6C0OI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_batch.table_test.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,5 @@ +chr1 23 31 PUM1,PUM1_3;1;mid1,did1 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;mid2,did2 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;mid2,did2 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;mid2,did2 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;mid2,did2 0 + 10.8788 0.000113 -1.0 -1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_batch.test_batch.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,5 @@ +chr1 23 31 PUM1,PUM1_3;1;method-id1,data-id1 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;method-id2,data-id2 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;method-id2,data-id2 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;method-id2,data-id2 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;method-id2,data-id2 0 + 10.8788 0.000113 -1.0 -1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_compare.test.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,479 @@ +chr21 43687623 43687629 PUM1_1;k562_eclip,human_v0.1,PUM1;clipper_idr,dewseq_w100_s5 0 + +chr21 8397362 8397368 PUM1_1;k562_eclip,human_v0.1,PUM1;clipper_idr,dewseq_w100_s5 0 + +chr21 8215042 8215048 PUM1_1;k562_eclip,human_v0.1,PUM1;clipper_idr 0 + +chr21 8215045 8215051 PUM1_1;k562_eclip,human_v0.1,PUM1;clipper_idr 0 + +chr21 8215075 8215081 PUM1_1;k562_eclip,human_v0.1,PUM1;clipper_idr 0 + +chr21 8214324 8214330 PUM1_1;k562_eclip,human_v0.1,PUM1;clipper_idr,dewseq_w100_s5 0 + +chr21 36375632 36375640 PUM1_2;k562_eclip,human_v0.1,PUM1;clipper_idr,dewseq_w100_s5 0 + +chr21 32764358 32764366 PUM1_2;k562_eclip,human_v0.1,PUM1;clipper_idr,dewseq_w100_s5 0 - +chr21 8214298 8214304 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8218698 8218704 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8214075 8214081 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8217841 8217847 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8217884 8217890 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8217961 8217967 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8217962 8217968 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8401737 8401743 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8397514 8397520 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8397534 8397540 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8397536 8397542 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8397540 8397546 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8397544 8397550 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8397554 8397560 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8397556 8397562 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8397680 8397686 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 8397336 8397342 PUM1_1;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 36375534 36375541 PUM1_3;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 36375556 36375563 PUM1_3;k562_eclip,human_v0.1,PUM1;dewseq_w100_s5 0 + +chr21 14371170 14371177 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14371168 14371175 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14371143 14371150 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734896 32734903 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734887 32734894 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734055 32734062 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734041 32734048 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961325 14961332 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 28945911 28945918 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr 0 - +chr21 33576754 33576761 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33576671 33576678 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33576685 33576692 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33576643 33576650 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36376310 36376317 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36376312 36376319 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 37223459 37223466 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 37203027 37203034 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 46569382 46569389 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36375544 36375551 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33560605 33560612 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14485730 14485737 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14485692 14485699 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 17789024 17789031 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 45602699 45602706 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 45602733 45602740 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 37515084 37515091 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 37515086 37515093 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 32628809 32628816 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 43761044 43761051 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 46324158 46324165 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 29345209 29345216 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099722 34099729 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099724 34099731 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099762 34099769 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 39175562 39175569 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 39175515 39175522 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34791779 34791786 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33524100 33524107 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 38156461 38156468 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 38823684 38823691 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33437440 33437447 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33437400 33437407 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33437428 33437435 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14961842 14961849 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961807 14961814 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961803 14961810 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961861 14961868 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 36376422 36376429 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 29326166 29326173 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 44861192 44861199 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14485254 14485261 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14485285 14485292 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34105602 34105609 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34105611 34105618 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34098705 34098712 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 32734647 32734654 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734638 32734645 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 44805668 44805675 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 44805641 44805648 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 44805634 44805641 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 37513892 37513899 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14961945 14961952 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887732 34887739 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887705 34887712 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887697 34887704 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887695 34887702 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33578071 33578078 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 43983059 43983066 PUM2_1;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14961325 14961332 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33504165 33504172 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33576612 33576619 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 37203027 37203034 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 45602708 45602715 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 32628809 32628816 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34099702 34099709 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 38156461 38156468 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 38823684 38823691 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33437400 33437407 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 29326166 29326173 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34105611 34105618 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 44805668 44805675 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961274 14961281 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 36375341 36375348 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 43983067 43983074 PUM2_2;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14371143 14371150 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734896 32734903 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734887 32734894 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734041 32734048 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961325 14961332 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 28945911 28945918 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr 0 - +chr21 33576671 33576678 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33576685 33576692 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33576643 33576650 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36376310 36376317 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 37203027 37203034 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 46569382 46569389 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36375544 36375551 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14485730 14485737 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14485692 14485699 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 17789024 17789031 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 45602733 45602740 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 32628809 32628816 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 46324158 46324165 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099724 34099731 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099762 34099769 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34791779 34791786 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33437440 33437447 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33437428 33437435 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14961842 14961849 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 29326166 29326173 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 44861192 44861199 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14485254 14485261 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14485285 14485292 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34098705 34098712 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 32734647 32734654 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734638 32734645 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 44805641 44805648 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 44805634 44805641 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 37513892 37513899 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14961945 14961952 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887732 34887739 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887705 34887712 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 43983059 43983066 PUM2_3;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14371143 14371150 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734887 32734894 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734041 32734048 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961325 14961332 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 28945911 28945918 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr 0 - +chr21 33576643 33576650 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36376310 36376317 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 37203027 37203034 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 17789024 17789031 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32628809 32628816 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 46324158 46324165 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099724 34099731 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099762 34099769 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 39175515 39175522 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33524055 33524062 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33437440 33437447 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14961842 14961849 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 29326166 29326173 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 29326130 29326137 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14485285 14485292 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961945 14961952 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887732 34887739 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887705 34887712 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 43983059 43983066 PUM2_4;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14371170 14371179 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14371143 14371152 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734896 32734905 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734887 32734896 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734885 32734894 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734879 32734888 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734041 32734050 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961325 14961334 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 28945911 28945920 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr 0 - +chr21 33576754 33576763 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33504165 33504174 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33576669 33576678 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33576683 33576692 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33576641 33576650 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36376308 36376317 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36376310 36376319 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36376343 36376352 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 37223459 37223468 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 37203025 37203034 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 46569388 46569397 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36375542 36375551 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 36375655 36375664 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 17789024 17789033 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 17789022 17789031 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 45602697 45602706 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 45602706 45602715 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 45602731 45602740 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 37515122 37515131 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 37515084 37515093 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 32628809 32628818 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 43761042 43761051 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 46324156 46324165 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 29345207 29345216 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099720 34099729 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099722 34099731 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34099760 34099769 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 39175562 39175571 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 39175515 39175524 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33524083 33524092 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33524047 33524056 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 33524030 33524039 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 38156459 38156468 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 43693415 43693424 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 43693399 43693408 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 38823682 38823691 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33437438 33437447 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33437398 33437407 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33437426 33437435 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14961842 14961851 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14961861 14961870 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 45512511 45512520 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33558832 33558841 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 44861192 44861201 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 14485285 14485294 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34105600 34105609 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 34105609 34105618 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 32734647 32734656 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734638 32734647 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 44805668 44805677 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 37513905 37513914 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 14961945 14961954 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 32734862 32734871 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887737 34887746 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887732 34887741 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887705 34887714 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887703 34887712 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887697 34887706 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 34887695 34887704 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 36375339 36375348 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 33578071 33578080 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 31671335 31671344 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 - +chr21 43983057 43983066 PUM2_5;k562_eclip,human_v0.1,PUM2;clipper_idr,dewseq_w100_s5 0 + +chr21 5240861 5240868 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14371383 14371390 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14371233 14371240 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14371201 14371208 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485810 14485817 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485768 14485775 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962220 14962227 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962047 14962054 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962038 14962045 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962036 14962043 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962034 14962041 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962032 14962039 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962030 14962037 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962028 14962035 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962026 14962033 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962024 14962031 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962022 14962029 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962020 14962027 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962018 14962025 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962016 14962023 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962005 14962012 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962003 14962010 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962001 14962008 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961999 14962006 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961997 14962004 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961777 14961784 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 17789055 17789062 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 28928381 28928388 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 28928377 28928384 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 29345791 29345798 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 31668867 31668874 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 31671211 31671218 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 32734630 32734637 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 32734626 32734633 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 32733935 32733942 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33437481 33437488 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33450630 33450637 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33450622 33450629 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33576727 33576734 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33558894 33558901 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560567 33560574 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560569 33560576 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560577 33560584 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560583 33560590 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560585 33560592 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560587 33560594 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34142958 34142965 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34100074 34100081 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34100076 34100083 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34788433 34788440 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 34788319 34788326 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 36375534 36375541 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375731 36375738 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375744 36375751 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375812 36375819 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375845 36375852 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 37223515 37223522 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 37223424 37223431 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 37223420 37223427 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 37515015 37515022 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 37514674 37514681 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823341 38823348 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823390 38823397 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823406 38823413 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 39175463 39175470 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988361 41988368 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988342 41988349 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988303 41988310 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 46569301 46569308 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 46569594 46569601 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 46569651 46569658 PUM2_1;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 14371383 14371390 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14371187 14371194 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485768 14485775 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961712 14961719 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961666 14961673 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 28928377 28928384 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 29326260 29326267 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34105530 34105537 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 37513708 37513715 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 44805847 44805854 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 46569651 46569658 PUM2_2;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 5240861 5240868 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485810 14485817 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485768 14485775 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962220 14962227 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962005 14962012 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 28928377 28928384 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 29345791 29345798 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 31668867 31668874 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 31671211 31671218 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 32733935 32733942 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33437481 33437488 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33450630 33450637 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33450622 33450629 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33560567 33560574 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560577 33560584 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34142958 34142965 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34788433 34788440 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 36375534 36375541 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375731 36375738 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375744 36375751 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375845 36375852 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 37223515 37223522 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 37223420 37223427 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 37515015 37515022 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 37514674 37514681 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823341 38823348 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 39175463 39175470 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988361 41988368 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988342 41988349 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988303 41988310 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 46569594 46569601 PUM2_3;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 5240861 5240868 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485810 14485817 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485768 14485775 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485393 14485400 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962220 14962227 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962178 14962185 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962005 14962012 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 28928377 28928384 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 28928347 28928354 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 29345791 29345798 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33450622 33450629 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33576568 33576575 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560567 33560574 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560577 33560584 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33578135 33578142 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 36375230 36375237 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375236 36375243 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375374 36375381 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375534 36375541 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 37514693 37514700 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823341 38823348 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 39175449 39175456 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988373 41988380 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988361 41988368 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988324 41988331 PUM2_4;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 5240861 5240870 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14371383 14371392 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14371231 14371240 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14371201 14371210 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485810 14485819 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485768 14485777 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14485719 14485728 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962220 14962229 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962045 14962054 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962038 14962047 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962036 14962045 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962034 14962043 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962032 14962041 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962030 14962039 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962028 14962037 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962026 14962035 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962024 14962033 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962022 14962031 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962020 14962029 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962018 14962027 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962016 14962025 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962014 14962023 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962005 14962014 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962003 14962012 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14962001 14962010 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961999 14962008 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961997 14962006 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961995 14962004 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961908 14961917 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961850 14961859 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961777 14961786 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 14961704 14961713 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 17789055 17789064 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 17789053 17789062 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 28928377 28928386 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 29345789 29345798 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 29326164 29326173 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 31668798 31668807 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 32734626 32734635 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 32734624 32734633 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 32733941 32733950 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 32733935 32733944 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33437493 33437502 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33450622 33450631 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33524156 33524165 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33524135 33524144 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 33576725 33576734 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33558869 33558878 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33558892 33558901 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560565 33560574 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560567 33560576 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560569 33560578 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560575 33560584 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560581 33560590 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560583 33560592 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560585 33560594 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 33560587 33560596 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34105653 34105662 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34098703 34098712 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34100072 34100081 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34100074 34100083 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34100082 34100091 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 34788319 34788328 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 34887755 34887764 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 36375372 36375381 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375532 36375541 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375742 36375751 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375810 36375819 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375812 36375821 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36375929 36375938 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 36376469 36376478 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 37223447 37223456 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 37223420 37223429 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 37515006 37515015 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 37514620 37514629 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 37514672 37514681 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823550 38823559 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823557 38823566 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823760 38823769 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823339 38823348 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823341 38823350 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823388 38823397 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823404 38823413 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 38823411 38823420 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 39175591 39175600 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 39175463 39175472 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988361 41988370 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988342 41988351 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 41988257 41988266 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 44805799 44805808 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 - +chr21 45602619 45602628 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 46569299 46569308 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 46569555 46569564 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 46569592 46569601 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 + +chr21 46569649 46569658 PUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_compare.test.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,480 @@ +combined_id motif_hit_id method_data_ids_with_hit +k562_eclip,human_v0.1,PUM1 chr21:43687623-43687629(+),PUM1_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397362-8397368(+),PUM1_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8215042-8215048(+),PUM1_1 clipper_idr +k562_eclip,human_v0.1,PUM1 chr21:8215045-8215051(+),PUM1_1 clipper_idr +k562_eclip,human_v0.1,PUM1 chr21:8215075-8215081(+),PUM1_1 clipper_idr +k562_eclip,human_v0.1,PUM1 chr21:8214324-8214330(+),PUM1_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:36375632-36375640(+),PUM1_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:32764358-32764366(-),PUM1_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8214298-8214304(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8218698-8218704(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8214075-8214081(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8217841-8217847(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8217884-8217890(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8217961-8217967(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8217962-8217968(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8401737-8401743(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397514-8397520(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397534-8397540(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397536-8397542(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397540-8397546(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397544-8397550(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397554-8397560(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397556-8397562(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397680-8397686(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:8397336-8397342(+),PUM1_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:36375534-36375541(+),PUM1_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM1 chr21:36375556-36375563(+),PUM1_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371170-14371177(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371168-14371175(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371143-14371150(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734896-32734903(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734887-32734894(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734055-32734062(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734041-32734048(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961325-14961332(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28945911-28945918(-),PUM2_1 clipper_idr +k562_eclip,human_v0.1,PUM2 chr21:33576754-33576761(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576671-33576678(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576685-33576692(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576643-33576650(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36376310-36376317(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36376312-36376319(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37223459-37223466(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37203027-37203034(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569382-46569389(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375544-36375551(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560605-33560612(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485730-14485737(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485692-14485699(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:17789024-17789031(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:45602699-45602706(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:45602733-45602740(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37515084-37515091(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37515086-37515093(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32628809-32628816(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:43761044-43761051(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46324158-46324165(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29345209-29345216(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099722-34099729(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099724-34099731(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099762-34099769(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175562-39175569(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175515-39175522(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34791779-34791786(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33524100-33524107(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38156461-38156468(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823684-38823691(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437440-33437447(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437400-33437407(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437428-33437435(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961842-14961849(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961807-14961814(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961803-14961810(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961861-14961868(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36376422-36376429(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29326166-29326173(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44861192-44861199(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485254-14485261(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485285-14485292(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34105602-34105609(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34105611-34105618(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34098705-34098712(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734647-32734654(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734638-32734645(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44805668-44805675(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44805641-44805648(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44805634-44805641(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37513892-37513899(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961945-14961952(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887732-34887739(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887705-34887712(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887697-34887704(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887695-34887702(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33578071-33578078(-),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:43983059-43983066(+),PUM2_1 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961325-14961332(-),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33504165-33504172(-),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576612-33576619(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37203027-37203034(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:45602708-45602715(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32628809-32628816(-),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099702-34099709(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38156461-38156468(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823684-38823691(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437400-33437407(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29326166-29326173(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34105611-34105618(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44805668-44805675(-),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961274-14961281(-),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375341-36375348(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:43983067-43983074(+),PUM2_2 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371143-14371150(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734896-32734903(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734887-32734894(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734041-32734048(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961325-14961332(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28945911-28945918(-),PUM2_3 clipper_idr +k562_eclip,human_v0.1,PUM2 chr21:33576671-33576678(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576685-33576692(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576643-33576650(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36376310-36376317(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37203027-37203034(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569382-46569389(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375544-36375551(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485730-14485737(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485692-14485699(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:17789024-17789031(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:45602733-45602740(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32628809-32628816(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46324158-46324165(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099724-34099731(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099762-34099769(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34791779-34791786(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437440-33437447(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437428-33437435(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961842-14961849(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29326166-29326173(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44861192-44861199(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485254-14485261(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485285-14485292(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34098705-34098712(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734647-32734654(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734638-32734645(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44805641-44805648(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44805634-44805641(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37513892-37513899(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961945-14961952(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887732-34887739(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887705-34887712(-),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:43983059-43983066(+),PUM2_3 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371143-14371150(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734887-32734894(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734041-32734048(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961325-14961332(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28945911-28945918(-),PUM2_4 clipper_idr +k562_eclip,human_v0.1,PUM2 chr21:33576643-33576650(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36376310-36376317(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37203027-37203034(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:17789024-17789031(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32628809-32628816(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46324158-46324165(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099724-34099731(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099762-34099769(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175515-39175522(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33524055-33524062(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437440-33437447(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961842-14961849(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29326166-29326173(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29326130-29326137(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485285-14485292(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961945-14961952(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887732-34887739(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887705-34887712(-),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:43983059-43983066(+),PUM2_4 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371170-14371179(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371143-14371152(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734896-32734905(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734887-32734896(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734885-32734894(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734879-32734888(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734041-32734050(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961325-14961334(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28945911-28945920(-),PUM2_5 clipper_idr +k562_eclip,human_v0.1,PUM2 chr21:33576754-33576763(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33504165-33504174(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576669-33576678(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576683-33576692(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576641-33576650(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36376308-36376317(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36376310-36376319(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36376343-36376352(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37223459-37223468(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37203025-37203034(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569388-46569397(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375542-36375551(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375655-36375664(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:17789024-17789033(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:17789022-17789031(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:45602697-45602706(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:45602706-45602715(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:45602731-45602740(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37515122-37515131(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37515084-37515093(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32628809-32628818(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:43761042-43761051(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46324156-46324165(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29345207-29345216(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099720-34099729(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099722-34099731(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34099760-34099769(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175562-39175571(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175515-39175524(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33524083-33524092(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33524047-33524056(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33524030-33524039(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38156459-38156468(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:43693415-43693424(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:43693399-43693408(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823682-38823691(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437438-33437447(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437398-33437407(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437426-33437435(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961842-14961851(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961861-14961870(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:45512511-45512520(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33558832-33558841(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44861192-44861201(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485285-14485294(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34105600-34105609(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34105609-34105618(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734647-32734656(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734638-32734647(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44805668-44805677(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37513905-37513914(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961945-14961954(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734862-32734871(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887737-34887746(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887732-34887741(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887705-34887714(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887703-34887712(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887697-34887706(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887695-34887704(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375339-36375348(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33578071-33578080(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:31671335-31671344(-),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:43983057-43983066(+),PUM2_5 clipper_idr,dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:5240861-5240868(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371383-14371390(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371233-14371240(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371201-14371208(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485810-14485817(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485768-14485775(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962220-14962227(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962047-14962054(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962038-14962045(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962036-14962043(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962034-14962041(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962032-14962039(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962030-14962037(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962028-14962035(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962026-14962033(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962024-14962031(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962022-14962029(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962020-14962027(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962018-14962025(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962016-14962023(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962005-14962012(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962003-14962010(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962001-14962008(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961999-14962006(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961997-14962004(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961777-14961784(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:17789055-17789062(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28928381-28928388(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28928377-28928384(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29345791-29345798(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:31668867-31668874(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:31671211-31671218(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734630-32734637(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734626-32734633(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32733935-32733942(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437481-33437488(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33450630-33450637(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33450622-33450629(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576727-33576734(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33558894-33558901(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560567-33560574(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560569-33560576(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560577-33560584(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560583-33560590(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560585-33560592(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560587-33560594(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34142958-34142965(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34100074-34100081(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34100076-34100083(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34788433-34788440(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34788319-34788326(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375534-36375541(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375731-36375738(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375744-36375751(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375812-36375819(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375845-36375852(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37223515-37223522(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37223424-37223431(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37223420-37223427(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37515015-37515022(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37514674-37514681(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823341-38823348(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823390-38823397(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823406-38823413(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175463-39175470(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988361-41988368(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988342-41988349(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988303-41988310(-),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569301-46569308(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569594-46569601(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569651-46569658(+),PUM2_1 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371383-14371390(-),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371187-14371194(-),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485768-14485775(-),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961712-14961719(-),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961666-14961673(-),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28928377-28928384(-),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29326260-29326267(+),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34105530-34105537(+),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37513708-37513715(+),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44805847-44805854(-),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569651-46569658(+),PUM2_2 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:5240861-5240868(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485810-14485817(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485768-14485775(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962220-14962227(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962005-14962012(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28928377-28928384(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29345791-29345798(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:31668867-31668874(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:31671211-31671218(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32733935-32733942(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437481-33437488(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33450630-33450637(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33450622-33450629(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560567-33560574(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560577-33560584(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34142958-34142965(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34788433-34788440(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375534-36375541(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375731-36375738(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375744-36375751(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375845-36375852(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37223515-37223522(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37223420-37223427(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37515015-37515022(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37514674-37514681(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823341-38823348(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175463-39175470(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988361-41988368(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988342-41988349(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988303-41988310(-),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569594-46569601(+),PUM2_3 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:5240861-5240868(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485810-14485817(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485768-14485775(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485393-14485400(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962220-14962227(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962178-14962185(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962005-14962012(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28928377-28928384(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28928347-28928354(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29345791-29345798(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33450622-33450629(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576568-33576575(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560567-33560574(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560577-33560584(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33578135-33578142(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375230-36375237(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375236-36375243(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375374-36375381(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375534-36375541(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37514693-37514700(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823341-38823348(+),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175449-39175456(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988373-41988380(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988361-41988368(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988324-41988331(-),PUM2_4 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:5240861-5240870(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371383-14371392(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371231-14371240(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14371201-14371210(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485810-14485819(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485768-14485777(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14485719-14485728(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962220-14962229(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962045-14962054(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962038-14962047(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962036-14962045(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962034-14962043(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962032-14962041(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962030-14962039(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962028-14962037(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962026-14962035(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962024-14962033(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962022-14962031(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962020-14962029(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962018-14962027(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962016-14962025(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962014-14962023(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962005-14962014(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962003-14962012(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14962001-14962010(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961999-14962008(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961997-14962006(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961995-14962004(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961908-14961917(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961850-14961859(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961777-14961786(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:14961704-14961713(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:17789055-17789064(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:17789053-17789062(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:28928377-28928386(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29345789-29345798(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:29326164-29326173(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:31668798-31668807(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734626-32734635(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32734624-32734633(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32733941-32733950(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:32733935-32733944(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33437493-33437502(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33450622-33450631(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33524156-33524165(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33524135-33524144(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33576725-33576734(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33558869-33558878(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33558892-33558901(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560565-33560574(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560567-33560576(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560569-33560578(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560575-33560584(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560581-33560590(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560583-33560592(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560585-33560594(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:33560587-33560596(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34105653-34105662(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34098703-34098712(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34100072-34100081(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34100074-34100083(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34100082-34100091(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34788319-34788328(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:34887755-34887764(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375372-36375381(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375532-36375541(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375742-36375751(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375810-36375819(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375812-36375821(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36375929-36375938(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:36376469-36376478(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37223447-37223456(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37223420-37223429(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37515006-37515015(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37514620-37514629(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:37514672-37514681(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823550-38823559(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823557-38823566(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823760-38823769(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823339-38823348(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823341-38823350(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823388-38823397(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823404-38823413(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:38823411-38823420(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175591-39175600(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:39175463-39175472(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988361-41988370(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988342-41988351(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:41988257-41988266(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:44805799-44805808(-),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:45602619-45602628(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569299-46569308(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569555-46569564(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569592-46569601(+),PUM2_5 dewseq_w100_s5 +k562_eclip,human_v0.1,PUM2 chr21:46569649-46569658(+),PUM2_5 dewseq_w100_s5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_search.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,5 @@ +chr1 23 31 PUM1,PUM1_3;1;method_id,data_id 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;method_id,data_id 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;method_id,data_id 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;method_id,data_id 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;method_id,data_id 0 + 10.8788 0.000113 -1.0 -1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_search.test_all.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,56 @@ +chr1 66 76 ACIN1,ACIN1_2;1;method_id,data_id 0 + 7.83168 0.000976 -1.0 -1.0 +chr1 35 42 ADAR,ADAR_2;1;method_id,data_id 0 + 7.76761 0.000162 -1.0 -1.0 +chr1 21 28 BUD13,BUD13_4;1;method_id,data_id 0 + 8.50505 0.000528 -1.0 -1.0 +chr1 16 23 CELF6,CELF6_1;1;method_id,data_id 0 + 7.54545 0.000859 -1.0 -1.0 +chr1 20 32 DDX6,DDX6_1;1;method_id,data_id 0 + 11.1616 5.8e-05 -1.0 -1.0 +chr1 47 53 DDX54,DDX54_2;1;method_id,data_id 0 + 10.0101 0.000506 -1.0 -1.0 +chr1 20 31 DGCR8,DGCR8_1;1;method_id,data_id 0 + 10.4646 0.000102 -1.0 -1.0 +chr1 57 64 ELAVL4,ELAVL4_1;1;method_id,data_id 0 + 8.90909 0.000307 -1.0 -1.0 +chr1 31 39 EWSR1,EWSR1_2;1;method_id,data_id 0 + 7.39394 0.000281 -1.0 -1.0 +chr1 25 35 FMR1,FMR1_1;1;method_id,data_id 0 + -1.28283 0.000939 -1.0 -1.0 +chr1 55 62 G3BP2,G3BP2_1;1;method_id,data_id 0 + 10.2323 0.00027 -1.0 -1.0 +chr1 20 29 GPKOW,GPKOW_1;1;method_id,data_id 0 + 7.56566 0.000629 -1.0 -1.0 +chr1 42 49 GPKOW,GPKOW_2;1;method_id,data_id 0 + 7.66337 0.000616 -1.0 -1.0 +chr1 13 20 HNRNPM,HNRNPM_2;1;method_id,data_id 0 + 9.36 0.000225 -1.0 -1.0 +chr1 65 74 LSM11,LSM11_4;1;method_id,data_id 0 + 7.32323 0.000681 -1.0 -1.0 +chr1 43 53 MTPAP,MTPAP_1;1;method_id,data_id 0 + 7.51485 0.000853 -1.0 -1.0 +chr1 65 75 NUP42,NUP42_1;1;method_id,data_id 0 + 7.56566 0.000678 -1.0 -1.0 +chr1 67 74 PABPC1,PABPC1_2;1;method_id,data_id 0 + 8.22 0.000763 -1.0 -1.0 +chr1 69 76 PABPC4,PABPC4_1;1;method_id,data_id 0 + 7.46 0.000936 -1.0 -1.0 +chr1 48 56 PCBP1,PCBP1_3;1;method_id,data_id 0 + 4.08081 0.00076 -1.0 -1.0 +chr1 35 41 PTBP1,PTBP1_5;1;method_id,data_id 0 + 9.37374 0.000653 -1.0 -1.0 +chr1 23 31 PUM1,PUM1_3;1;method_id,data_id 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;method_id,data_id 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;method_id,data_id 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;method_id,data_id 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;method_id,data_id 0 + 10.8788 0.000113 -1.0 -1.0 +chr1 35 47 QKI,QKI_4;1;method_id,data_id 0 + -5.90909 0.000181 -1.0 -1.0 +chr1 35 44 RBM5,RBM5_1;1;method_id,data_id 0 + 7.52525 5.21e-05 -1.0 -1.0 +chr1 60 67 RC3H1,RC3H1_2;1;method_id,data_id 0 + 7.76768 0.000997 -1.0 -1.0 +chr1 13 27 TROVE2,TROVE2_2;1;method_id,data_id 0 + -20.1313 0.00042 -1.0 -1.0 +chr1 27 41 TROVE2,TROVE2_2;1;method_id,data_id 0 + -20.1919 0.000704 -1.0 -1.0 +chr1 32 40 TROVE2,TROVE2_5;1;method_id,data_id 0 + 8.83 0.000368 -1.0 -1.0 +chr1 59 72 TROVE2,TROVE2_7;1;method_id,data_id 0 + -12.6061 0.000794 -1.0 -1.0 +chr1 65 76 SAFB2,SAFB2_1;1;method_id,data_id 0 + 6.32 0.00098 -1.0 -1.0 +chr1 67 74 SART3,SART3_1;1;method_id,data_id 0 + 8.22 0.000763 -1.0 -1.0 +chr1 18 29 SF3A3,SF3A3_1;1;method_id,data_id 0 + 7.58416 0.000793 -1.0 -1.0 +chr1 35 46 SF3A3,SF3A3_1;1;method_id,data_id 0 + 10.3168 0.000128 -1.0 -1.0 +chr1 32 40 SF3A3,SF3A3_4;1;method_id,data_id 0 + 9.57 0.000254 -1.0 -1.0 +chr1 22 30 SF3B4,SF3B4_1;1;method_id,data_id 0 + 7.34 0.000985 -1.0 -1.0 +chr1 43 51 SRSF1,SRSF1_4;1;method_id,data_id 0 + 7.93939 0.000678 -1.0 -1.0 +chr1 50 59 SRSF2,SRSF2_8;1;method_id,data_id 0 + 11.4646 5.89e-05 -1.0 -1.0 +chr1 44 53 SRSF4,SRSF4_1;1;method_id,data_id 0 + 8.28283 0.000231 -1.0 -1.0 +chr1 44 52 SRSF5,SRSF5_1;1;method_id,data_id 0 + 3.93939 0.000409 -1.0 -1.0 +chr1 68 76 SRSF5,SRSF5_1;1;method_id,data_id 0 + 10.8081 0.0002 -1.0 -1.0 +chr1 67 78 SRSF7,SRSF7_2;1;method_id,data_id 0 + 7.27723 0.000652 -1.0 -1.0 +chr1 12 21 TAF15,TAF15_3;1;method_id,data_id 0 + 7.19 0.000808 -1.0 -1.0 +chr1 42 51 TRA2A,TRA2A_5;1;method_id,data_id 0 + 7.68317 0.000727 -1.0 -1.0 +chr1 26 33 TUT1,TUT1_1;1;method_id,data_id 0 + 9.56566 0.000191 -1.0 -1.0 +chr1 26 33 TUT1,TUT1_2;1;method_id,data_id 0 + 9.56566 0.000191 -1.0 -1.0 +chr1 36 45 U2AF1,U2AF1_1;1;method_id,data_id 0 + 10.03 0.000165 -1.0 -1.0 +chr1 36 45 U2AF2,U2AF2_1;1;method_id,data_id 0 + 9.9697 0.000192 -1.0 -1.0 +chr1 25 32 UNK,UNK_2;1;method_id,data_id 0 + 7.78 0.000861 -1.0 -1.0 +chr1 60 68 ZFP36,ZFP36_1;1;method_id,data_id 0 + 9.28 0.000317 -1.0 -1.0 +chr1 59 68 ZFP36L2,ZFP36L2_1;1;method_id,data_id 0 + 8.33333 0.000104 -1.0 -1.0 +chr1 59 68 ZFP36L2,ZFP36L2_2;1;method_id,data_id 0 + 8.33333 0.000104 -1.0 -1.0 +chr1 28 46 SLBP,RF00032;1;method_id,data_id 0 + 13.8 4.2e-05 -1.0 -1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.compare_test.clipper_idr.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +k562_eclip clipper_idr run_id human_v0.1 PUM1 32 65.03 61 10 202 2081 2081 6 18.75 8 8 56 2.691013935607881 2.691013935607881 3.8443056222969725 3.8443056222969725 0.12193332097392165 PUM1_1,PUM1_2,PUM1_3 6,2,0 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 PUM2 77 60.66 55 3 172 4671 4671 59 76.62337662337663 219 219 824 17.64076214943267 17.64076214943267 46.88503532434168 46.88503532434168 0.4736101622265477 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 68,16,39,24,72 - - AJ40lTA6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.compare_test.dewseq.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +k562_eclip dewseq_w100_s5 run_id human_v0.1 PUM1 23 214.74 195 68 850 4939 4750 10 43.47826086956522 24 24 152 3.0775460619558612 3.2 4.859283255719781 5.052631578947368 0.0071490418994820636 PUM1_1,PUM1_2,PUM1_3 20,2,2 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 PUM2 70 203.41 187 100 745 14239 12333 65 92.85714285714286 559 448 1737 12.198890371514853 14.084164436876673 31.46288362946836 36.32530608935377 0.9472904311972452 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 138,27,69,48,166 - - -sbAn7Po
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.rbpbench_search.slbp_user.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,2 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +data_id method_id run_id user SLBP_USER 1 63 63 63 63 63 63 1 100.0 1 1 25 39.682539682539684 39.682539682539684 15.873015873015873 15.873015873015873 1.0 - - RF00032 1 RuDIjV1k
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.rbpbench_search.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +data_id method_id run_id human_v0.1 PUM1 1 70 70 70 70 70 70 1 100.0 1 1 8 11.428571428571429 11.428571428571429 14.285714285714285 14.285714285714285 1.0 PUM1_1,PUM1_2,PUM1_3 0,0,1 - - h2FelLqa +data_id method_id run_id human_v0.1 PUM2 1 70 70 70 70 70 70 1 100.0 4 4 10 14.285714285714285 14.285714285714285 57.14285714285714 57.14285714285714 1.0 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 1,0,1,1,1 - - HcD7_nJz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.table_test.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +did1 mid1 run_id human_v0.1 PUM1 1 70 70 70 70 70 70 1 100.0 1 1 8 11.428571428571429 11.428571428571429 14.285714285714285 14.285714285714285 1.0 PUM1_1,PUM1_2,PUM1_3 0,0,1 - - NInGOqIN +did2 mid2 run_id human_v0.1 PUM2 1 70 70 70 70 70 70 1 100.0 4 4 10 14.285714285714285 14.285714285714285 57.14285714285714 57.14285714285714 1.0 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 1,0,1,1,1 - - u7eY1SoG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.test_batch.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +data-id1 method-id1 run_id human_v0.1 PUM1 1 70 70 70 70 70 70 1 100.0 1 1 8 11.428571428571429 11.428571428571429 14.285714285714285 14.285714285714285 1.0 PUM1_1,PUM1_2,PUM1_3 0,0,1 - - TT41sPJM +data-id2 method-id2 run_id human_v0.1 PUM2 1 70 70 70 70 70 70 1 100.0 4 4 10 14.285714285714285 14.285714285714285 57.14285714285714 57.14285714285714 1.0 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 1,0,1,1,1 - - -dJ6C0OI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.rbpbench_compare.test.html Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,98 @@ +<p><head> +<title>RBPBench - Motif Search Comparison Report</title></p> +<script src="/home/malong/miniconda3/envs/rbpbench/lib/python3.9/site-packages/rbpbench/content/sorttable.js" type="text/javascript"></script> +<p></head></p> +<h1>Comparison Report</h1> +<p>List of available comparison statistics generated +by RBPBench (rbpbench compare):</p> +<ul> +<li><a href="#method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison table</a></li> +<li><a href="#method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison table</a></li> +<li><a href="#method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</a></li> +<li><a href="#method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</a></li> +</ul> +<p> </p> +<h2 id="method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison statistics</h2> +<p><strong>Table:</strong> RBP motif hit statistics for combined ID "k562_eclip,human_v0.1,PUM1" (data ID, motif database ID, RBP ID) over different methods (method ID column).</p> +<table class="sortable"> +<thead> +<tr> +<th style="text-align: center;">Method ID</th> +<th style="text-align: center;"># regions</th> +<th style="text-align: center;"># motif hits</th> +<th style="text-align: center;">% regions with motifs</th> +<th style="text-align: center;">% motif nucleotides</th> +<th style="text-align: center;"># motif hits per 1000 nt</th> +</tr> +</thead> +<tbody> +<tr> +<td style="text-align: center;">dewseq_w100_s5</td> +<td style="text-align: center;">23</td> +<td style="text-align: center;">24</td> +<td style="text-align: center;">43.48</td> +<td style="text-align: center;">3.20</td> +<td style="text-align: center;">4.86</td> +</tr> +<tr> +<td style="text-align: center;">clipper_idr</td> +<td style="text-align: center;">32</td> +<td style="text-align: center;">8</td> +<td style="text-align: center;">18.75</td> +<td style="text-align: center;">2.69</td> +<td style="text-align: center;">3.84</td> +</tr> +</tbody> +</table> +<p> + </p> +<p>Column IDs have the following meanings: <strong>Method ID</strong> -> method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -> number of peak regions used for motif search, <strong># motif hits</strong> -> number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -> percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -> percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -> number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p> +<h2 id="method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison statistics</h2> +<p><strong>Table:</strong> RBP motif hit statistics for combined ID "k562_eclip,human_v0.1,PUM2" (data ID, motif database ID, RBP ID) over different methods (method ID column).</p> +<table class="sortable"> +<thead> +<tr> +<th style="text-align: center;">Method ID</th> +<th style="text-align: center;"># regions</th> +<th style="text-align: center;"># motif hits</th> +<th style="text-align: center;">% regions with motifs</th> +<th style="text-align: center;">% motif nucleotides</th> +<th style="text-align: center;"># motif hits per 1000 nt</th> +</tr> +</thead> +<tbody> +<tr> +<td style="text-align: center;">dewseq_w100_s5</td> +<td style="text-align: center;">70</td> +<td style="text-align: center;">448</td> +<td style="text-align: center;">92.86</td> +<td style="text-align: center;">14.08</td> +<td style="text-align: center;">31.46</td> +</tr> +<tr> +<td style="text-align: center;">clipper_idr</td> +<td style="text-align: center;">77</td> +<td style="text-align: center;">219</td> +<td style="text-align: center;">76.62</td> +<td style="text-align: center;">17.64</td> +<td style="text-align: center;">46.89</td> +</tr> +</tbody> +</table> +<p> + </p> +<p>Column IDs have the following meanings: <strong>Method ID</strong> -> method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -> number of peak regions used for motif search, <strong># motif hits</strong> -> number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -> percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -> percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -> number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p> +<h2 id="method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</h2> +<p>Based on the same combined ID "k562_eclip,human_v0.1,PUM1" (data ID, motif database ID, RBP ID), motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) are compared via Venn diagram. +Any given motif hit can either be found only by one method, or be identified by any set (>=2) of methods (intersection areas).</p> +<p><img src="html_report_plots/venn_diagram.method_comp.k562_eclip,human_v0.1,PUM1.png" alt="dataset comparison plot k562_eclip,human_v0.1,PUM1 +title="dataset comparison plot k562_eclip,human_v0.1,PUM1" width="700" /></p> +<p><strong>Figure:</strong> Venn diagram of motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) with identical combined ID (k562_eclip,human_v0.1,PUM1) + corresponding percentages of total motif hits for each region (method exclusive and intersection(s)).</p> +<p> </p> +<h2 id="method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</h2> +<p>Based on the same combined ID "k562_eclip,human_v0.1,PUM2" (data ID, motif database ID, RBP ID), motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) are compared via Venn diagram. +Any given motif hit can either be found only by one method, or be identified by any set (>=2) of methods (intersection areas).</p> +<p><img src="html_report_plots/venn_diagram.method_comp.k562_eclip,human_v0.1,PUM2.png" alt="dataset comparison plot k562_eclip,human_v0.1,PUM2 +title="dataset comparison plot k562_eclip,human_v0.1,PUM2" width="700" /></p> +<p><strong>Figure:</strong> Venn diagram of motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) with identical combined ID (k562_eclip,human_v0.1,PUM2) + corresponding percentages of total motif hits for each region (method exclusive and intersection(s)).</p> +<p> </p>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.rbpbench_search.html Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,83 @@ +<p><head> +<title>RBPBench - Search Report</title></p> +<script src="/home/uhlm/Programme/miniconda3/envs/rbpbench/lib/python3.11/site-packages/rbpbench/content/sorttable.js" type="text/javascript"></script> +<p></head></p> +<h1>Search report</h1> +<p>List of available statistics and plots generated +by RBPBench (rbpbench search --report):</p> +<ul> +<li><a href="#rbp-enrich-stats">RBP motif enrichment statistics</a></li> +<li><a href="#cooc-heat-map">RBP co-occurrences heat map</a></li> +<li><a href="#corr-heat-map">RBP correlations heat map</a> + </li> +</ul> +<h2 id="rbp-enrich-stats">RBP motif enrichment statistics</h2> +<p><strong>Table:</strong> RBP motif enrichment statistics. Given a score for each genomic region (# input regions = 1), +RBPbench checks whether motifs are enriched +in higher-scoring regions (using Wilcoxon rank-sum test). A low Wilcoxon rank-sum test p-value for a given RBP thus indicates +that higher-scoring regions are more likely to contain motif hits of the respective RBP. NOTE that if scores associated to +input genomic regions are all the same, p-values become meaningless (i.e., they result in p-values of 1.0).</p> +<table class="sortable"> +<thead> +<tr> +<th style="text-align: center;">RBP ID</th> +<th style="text-align: center;"># hit regions</th> +<th style="text-align: center;">% hit regions</th> +<th style="text-align: center;"># motif hits</th> +<th style="text-align: center;">p-value</th> +</tr> +</thead> +<tbody> +<tr> +<td style="text-align: center;">PUM1</td> +<td style="text-align: center;">1</td> +<td style="text-align: center;">100.00</td> +<td style="text-align: center;">1</td> +<td style="text-align: center;">1.0</td> +</tr> +<tr> +<td style="text-align: center;">PUM2</td> +<td style="text-align: center;">1</td> +<td style="text-align: center;">100.00</td> +<td style="text-align: center;">4</td> +<td style="text-align: center;">1.0</td> +</tr> +</tbody> +</table> +<p> + </p> +<p>Column IDs have the following meanings: <strong>RBP ID</strong> -> RBP ID from database or user-defined (typically RBP name), <strong># hit regions</strong> -> number of input genomic regions with motif hits (after filtering and optional extension), <strong>% hit regions</strong> -> percentage of hit regions over all regions (i.e. how many input regions contain >= 1 RBP binding motif), <strong># motif hits</strong> -> number of unique motif hits in input regions (removed double counts), <strong>p-value</strong> -> Wilcoxon rank-sum test p-value.</p> +<h2 id="cooc-heat-map">RBP co-occurrences heat map</h2> +<p>RBP co-occurrences heat map.</p> +<div class=class="container-fluid" style="margin-top:40px"> +<iframe src="html_report_plots/co-occurrence_plot.plotly.html" width="1200" height="1200"></iframe> +</div> + +<p><strong>Figure:</strong> Heat map of co-occurrences (Fisher's exact test p-values) between RBPs. +Legend color: negative logarithm (base 10) of Fisher's exact test p-value. +Hover box: 1) RBP1. 2) RBP2. 3) p-value: Fisher's exact test p-value (calculated based on contingency table between RBP1 and RBP2). +4) RBPs compaired. 5) Counts[]: Contingency table of co-occurrence counts (i.e., number of genomic regions with/without shared motif hits) between compaired RBPs, +with format [[A, B], [C, D]], where +A: RBP1 AND RBP2, +B: NOT RBP1 AND RBP2 +C: RBP1 AND NOT RBP2 +D: NOT RBP1 AND NOT RBP2. </p> +<p> </p> +<h2 id="corr-heat-map">RBP correlations heat map</h2> +<p>RBP correlations heat map.</p> +<div class=class="container-fluid" style="margin-top:40px"> +<iframe src="html_report_plots/correlation_plot.plotly.html" width="1200" height="1200"></iframe> +</div> + +<p><strong>Figure:</strong> Heat map of correlations (Pearson correlation coefficients) between RBPs. +Genomic regions are labelled 1 or 0 (RBP motif present or not), resulting in a vector of 1s and 0s for each RBP. +Correlations are then calculated by comparing vectors for every pair of RBPs. +Legend color: Pearson correlation coefficient. +Hover box: 1) RBP1. 2) RBP2. +3) RBPs compaired. 5) Counts[]: Contingency table of co-occurrence counts (i.e., number of genomic regions with/without shared motif hits) between compaired RBPs, +with format [[A, B], [C, D]], where +A: RBP1 AND RBP2, +B: NOT RBP1 AND RBP2 +C: RBP1 AND NOT RBP2 +D: NOT RBP1 AND NOT RBP2. </p> +<p> </p>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,1 @@ +chr1 10 80 PUM1_K562_IDR 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fa Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,2 @@ +>chr1 +TCTTATTAATACTGGTTGTGATTTGTAGATACTGGCTCTTCTCAGATGAAGTTCCAGGATTATTCATTGAAAAAGGCTGGGTACATGAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.slbp_user.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,1 @@ +chr1 50 113 SLBP_K562_IDR 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.slbp_user.fa Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,2 @@ +>chr1 +AACATCCAGGCTGTGCTACTGCCCAAGAAGACCGAGAGTCACCACAAGGCCAAAGGCAAATAATGTCTCCATAGAATCACTTTCCAATACAACGGCTCTTTTCAGAGCCACCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,1 @@ +chr1 10 80 PUM1_K562_IDR 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,1 @@ +chr1 10 80 PUM1_K562_IDR 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_custom.info.txt Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,10 @@ +RBP_motif_id RBP_name Motif_type Organism +PUM1_1 PUM1 meme_xml human +PUM1_2 PUM1 meme_xml human +PUM1_3 PUM1 meme_xml human +PUM2_1 PUM2 meme_xml human +PUM2_2 PUM2 meme_xml human +PUM2_3 PUM2 meme_xml human +PUM2_4 PUM2 meme_xml human +PUM2_5 PUM2 meme_xml human +RF00032 SLBP cm human
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_custom.motif_hits.rbpbench_search.bed Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,6 @@ +chr1 23 31 PUM1,PUM1_3;1;method_id,data_id 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;method_id,data_id 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;method_id,data_id 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;method_id,data_id 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;method_id,data_id 0 + 10.8788 0.000113 -1.0 -1.0 +chr1 28 46 SLBP,RF00032;1;method_id,data_id 0 + 13.8 4.2e-05 -1.0 -1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_custom.seq_motifs.meme Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,99 @@ +MEME version 5 + +ALPHABET= ACGT + +strands: + + +Background letter frequencies +A 0.250000 C 0.250000 G 0.250000 T 0.250000 + +MOTIF PUM1_1 +letter-probability matrix: alength= 4 w= 7 nsites= 20 E= 0 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.223900 0.184800 0.212700 0.378600 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.835718 0.164282 + 0.041300 0.041200 0.876300 0.041200 + +MOTIF PUM1_2 +letter-probability matrix: alength= 4 w= 9 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 0.500000 0.500000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.500000 0.000000 0.500000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 0.000000 1.000000 + +MOTIF PUM1_3 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.919505 0.080495 0.000000 0.000000 + 0.145800 0.458500 0.168500 0.227200 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.100031 0.899969 + 0.867950 0.132050 0.000000 0.000000 + +MOTIF PUM2_1 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.397900 0.158200 0.026000 0.417900 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.843493 0.000000 0.000000 0.156507 + +MOTIF PUM2_2 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 1.000000 0.000000 0.000000 + +MOTIF PUM2_3 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + +MOTIF PUM2_4 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 1.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + +MOTIF PUM2_5 +letter-probability matrix: alength= 4 w= 10 nsites= 20 E= 0 + 0.253775 0.137486 0.112989 0.495750 + 0.270800 0.141400 0.146600 0.441200 + 0.000000 0.000000 0.000000 1.000000 + 0.072132 0.000000 0.896223 0.031646 + 0.000000 0.000000 0.000000 1.000000 + 0.968974 0.000000 0.031026 0.000000 + 0.232400 0.319800 0.028700 0.419100 + 0.932355 0.000000 0.000000 0.067645 + 0.121986 0.000000 0.173847 0.704167 + 0.517200 0.063500 0.123600 0.295700 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_custom.str_motifs.cm Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,385 @@ +INFERNAL1/a [1.1.3 | Nov 2019] +NAME Histone3 +ACC RF00032 +DESC Histone 3' UTR stem-loop +STATES 142 +NODES 42 +CLEN 46 +W 57 +ALPH RNA +RF no +CONS yes +MAP yes +DATE Fri Apr 4 13:03:46 2014 +COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED +COM [2] /nfs/production/xfam/rfam/software/bin/cmcalibrate --mpi CM +PBEGIN 0.05 +PEND 0.05 +WBETA 1e-07 +QDBBETA1 1e-07 +QDBBETA2 1e-15 +N2OMEGA 1.52588e-05 +N3OMEGA 1.52588e-05 +ELSELF -0.08926734 +NSEQ 46 +EFFN 46.000000 +CKSUM 471917655 +NULL 0.000 0.000 0.000 0.000 +GA 25.00 +TC 25.00 +NC 24.90 +EFP7GF -8.9961 0.74543 +ECMLC 0.73248 -4.63583 3.49505 1600000 463131 0.002591 +ECMGC 0.50982 -9.05666 1.92502 1600000 108029 0.003703 +ECMLI 0.86412 -1.32523 4.80439 1600000 239617 0.005008 +ECMGI 0.55516 -6.80684 2.91667 1600000 88393 0.004525 +CM + [ ROOT 0 ] - - - - - - + S 0 -1 0 1 4 1 1 57 76 -10.705 -10.912 -0.004 -9.326 + IL 1 1 2 1 4 1 19 64 83 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 + IR 2 2 3 2 3 1 19 63 81 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 1 ] 1 - c - - - + ML 3 2 3 5 3 1 19 57 76 -11.622 -0.002 -10.276 0.274 0.676 -1.683 -0.183 + D 4 2 3 5 3 0 15 58 76 -6.174 -1.687 -0.566 + IL 5 5 3 5 3 1 18 62 80 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 2 ] 2 - c - - - + ML 6 5 3 8 3 1 18 56 75 -11.622 -0.002 -10.276 0.562 0.685 -1.974 -0.595 + D 7 5 3 8 3 0 15 57 75 -6.174 -1.687 -0.566 + IL 8 8 3 8 3 1 17 61 79 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 3 ] 3 - A - - - + ML 9 8 3 11 3 1 17 55 74 -11.622 -0.002 -10.276 1.588 -1.105 -4.684 -1.031 + D 10 8 3 11 3 0 14 56 74 -6.174 -1.687 -0.566 + IL 11 11 3 11 3 1 17 60 78 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 4 ] 4 - A - - - + ML 12 11 3 14 3 1 16 54 73 -11.622 -0.002 -10.276 1.035 -0.025 -1.895 -0.517 + D 13 11 3 14 3 0 14 55 73 -6.174 -1.687 -0.566 + IL 14 14 3 14 3 1 16 59 77 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 5 ] 5 - a - - - + ML 15 14 3 17 3 1 15 53 72 -11.923 -0.687 -1.402 0.970 0.662 -4.530 -1.266 + D 16 14 3 17 3 0 14 52 71 -5.620 -0.734 -1.403 + IL 17 17 3 17 3 1 15 55 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 6 ] - 47 - U - - + MR 18 17 3 20 3 1 14 52 71 -11.239 -0.003 -9.556 -1.280 -3.255 -0.399 1.446 + D 19 17 3 20 3 0 13 51 70 -11.650 -0.025 -5.880 + IR 20 20 3 20 3 1 12 54 72 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 7 ] - 46 - g - - + MR 21 20 3 23 3 1 14 51 70 -11.923 -0.002 -10.241 0.333 -0.456 0.341 -0.425 + D 22 20 3 23 3 0 8 50 68 -6.390 -1.568 -0.620 + IR 23 23 3 23 3 1 12 53 71 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 8 ] - 45 - U - - + MR 24 23 3 26 3 1 13 50 69 -11.923 -0.002 -10.241 0.022 -0.397 -2.351 1.021 + D 25 23 3 26 3 0 7 49 67 -6.390 -1.568 -0.620 + IR 26 26 3 26 3 1 11 52 70 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 9 ] - 44 - u - - + MR 27 26 3 29 3 1 12 49 68 -11.923 -0.002 -10.241 0.188 -0.473 -0.169 0.323 + D 28 26 3 29 3 0 6 48 66 -6.390 -1.568 -0.620 + IR 29 29 3 29 3 1 10 51 69 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 10 ] - 43 - u - - + MR 30 29 3 32 3 1 11 48 67 -11.923 -0.002 -10.241 0.043 -1.204 0.229 0.448 + D 31 29 3 32 3 0 5 47 65 -6.390 -1.568 -0.620 + IR 32 32 3 32 3 1 10 50 68 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 11 ] - 42 - u - - + MR 33 32 3 35 3 1 10 47 66 -11.923 -0.037 -5.328 0.283 -0.639 -0.668 0.596 + D 34 32 3 35 3 0 5 46 64 -6.390 -1.568 -0.620 + IR 35 35 3 35 3 1 9 49 67 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 12 ] - 41 - a - - + MR 36 35 3 38 3 1 9 46 65 -11.888 -0.002 -10.205 0.690 -2.247 0.302 -0.084 + D 37 35 3 38 3 0 4 45 64 -8.147 -0.315 -2.376 + IR 38 38 3 38 3 1 7 48 66 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 13 ] - 40 - a - - + MR 39 38 3 41 3 1 8 45 64 -11.923 -0.002 -10.241 0.896 -0.277 -0.185 -1.204 + D 40 38 3 41 3 0 2 44 62 -6.390 -1.568 -0.620 + IR 41 41 3 41 3 1 6 47 65 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 14 ] - 39 - A - - + MR 42 41 3 44 3 1 7 44 63 -11.923 -0.002 -10.241 1.147 -1.015 -0.320 -1.029 + D 43 41 3 44 3 0 1 43 61 -6.390 -1.568 -0.620 + IR 44 44 3 44 3 1 5 46 64 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 15 ] - 38 - a - - + MR 45 44 3 47 3 1 7 43 62 -11.923 -0.027 -5.794 0.871 -0.426 -0.479 -0.497 + D 46 44 3 47 3 0 1 42 60 -6.390 -1.568 -0.620 + IR 47 47 3 47 3 1 5 45 63 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 16 ] - 37 - a - - + MR 48 47 3 50 3 1 6 42 61 -11.898 -0.002 -10.216 0.726 -0.863 -0.477 0.109 + D 49 47 3 50 3 0 0 41 60 -7.823 -0.406 -2.053 + IR 50 50 3 50 3 1 3 44 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 17 ] - 36 - a - - + MR 51 50 3 53 3 1 5 41 60 -11.923 -0.002 -10.241 0.725 -1.911 -0.230 0.297 + D 52 50 3 53 3 0 0 40 58 -6.390 -1.568 -0.620 + IR 53 53 3 53 3 1 3 43 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 18 ] - 35 - a - - + MR 54 53 3 56 3 1 4 40 59 -11.923 -0.002 -10.241 0.828 -0.827 -1.719 0.441 + D 55 53 3 56 3 0 0 39 57 -6.390 -1.568 -0.620 + IR 56 56 3 56 3 1 2 42 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 19 ] - 34 - c - - + MR 57 56 3 59 3 1 3 39 58 -11.923 -0.002 -10.241 0.119 0.695 -0.517 -0.745 + D 58 56 3 59 3 0 0 38 56 -6.390 -1.568 -0.620 + IR 59 59 3 59 3 1 2 41 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 20 ] - 33 - a - - + MR 60 59 3 62 3 1 2 38 57 -11.923 -0.002 -10.241 0.569 -0.255 -1.396 0.378 + D 61 59 3 62 3 0 0 37 55 -6.390 -1.568 -0.620 + IR 62 62 3 62 3 1 1 40 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 21 ] - 32 - u - - + MR 63 62 3 65 3 1 1 37 56 -11.923 -0.056 -4.714 0.347 -0.205 -0.853 0.387 + D 64 62 3 65 3 0 0 36 54 -6.390 -1.568 -0.620 + IR 65 65 3 65 3 1 1 39 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 22 ] - 31 - u - - + MR 66 65 3 68 3 1 3 36 55 -11.868 -0.002 -10.186 0.706 -1.486 -1.611 0.752 + D 67 65 3 68 3 0 0 35 54 -8.618 -0.220 -2.847 + IR 68 68 3 68 3 1 1 38 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 23 ] - 30 - u - - + MR 69 68 3 71 3 1 2 35 54 -11.923 -0.002 -10.241 -0.972 -0.369 0.214 0.638 + D 70 68 3 71 3 0 0 34 52 -6.390 -1.568 -0.620 + IR 71 71 3 71 3 1 1 37 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 24 ] - 29 - A - - + MR 72 71 3 74 3 1 1 34 53 -11.923 -0.047 -4.982 1.166 -1.748 -1.275 0.063 + D 73 71 3 74 3 0 0 33 52 -6.390 -1.568 -0.620 + IR 74 74 3 74 3 1 1 36 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 25 ] - 28 - c - - + MR 75 74 3 77 3 1 1 33 52 -11.878 -0.002 -10.195 -0.910 0.584 -0.997 0.554 + D 76 74 3 77 3 0 0 32 51 -8.406 -0.258 -2.636 + IR 77 77 3 77 3 1 1 35 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 26 ] - 27 - A - - + MR 78 77 3 80 3 1 1 32 51 -11.923 -0.071 -4.384 1.458 -1.557 -2.019 -0.586 + D 79 77 3 80 3 0 0 31 50 -6.390 -1.568 -0.620 + IR 80 80 3 80 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 27 ] - 26 - a - - + MR 81 80 3 83 3 1 1 31 50 -1.344 -0.725 -10.171 0.698 0.567 -2.058 -0.607 + D 82 80 3 83 3 0 0 31 49 -0.277 -4.066 -3.118 + IR 83 83 3 83 3 1 1 31 49 -6.042 -0.027 -8.281 0.000 0.000 0.000 0.000 + [ MATR 28 ] - 24 - c - - + MR 84 83 3 86 3 1 1 30 48 -11.923 -0.002 -10.241 0.331 0.903 -2.658 -0.486 + D 85 83 3 86 3 0 0 29 47 -6.390 -1.568 -0.620 + IR 86 86 3 86 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 29 ] - 23 - C - - + MR 87 86 3 89 3 1 1 29 47 -11.923 -0.002 -10.241 -2.740 1.578 -5.132 -0.259 + D 88 86 3 89 3 0 0 28 46 -6.390 -1.568 -0.620 + IR 89 89 3 89 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 + [ MATR 30 ] - 22 - A - - + MR 90 89 3 92 5 1 1 28 46 -10.571 -0.003 -10.387 -10.599 -11.491 1.957 -3.517 -6.202 -6.036 + D 91 89 3 92 5 0 0 27 45 -5.352 -0.707 -2.978 -4.409 -2.404 + IR 92 92 3 92 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 31 ] 6 21 G C - - + MP 93 92 3 97 6 2 2 27 45 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -9.446 -6.202 -11.294 -3.624 -11.134 -7.406 -5.494 -10.940 -7.562 3.944 -7.769 -1.149 -5.842 -7.856 -7.917 -10.190 + ML 94 92 3 97 6 1 1 26 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 95 92 3 97 6 1 1 25 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 96 92 3 97 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 97 97 5 97 6 1 1 27 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 98 98 6 98 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 32 ] 7 20 G C - - + MP 99 98 6 103 6 2 2 25 43 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -9.520 -6.204 -11.599 -3.658 -11.128 -7.383 -5.483 -11.144 -7.569 3.980 -7.767 -4.127 -5.848 -7.844 -7.915 -10.583 + ML 100 98 6 103 6 1 1 24 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 101 98 6 103 6 1 1 24 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 102 98 6 103 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 103 103 5 103 6 1 1 25 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 104 104 6 104 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 33 ] 8 19 C G - - + MP 105 104 6 109 6 2 2 23 41 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -8.195 -8.273 -7.664 0.485 -6.102 -7.918 3.494 -6.975 -7.717 -4.266 -7.912 -6.303 1.648 -8.123 -3.772 -6.505 + ML 106 104 6 109 6 1 1 22 41 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 107 104 6 109 6 1 1 22 41 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 108 104 6 109 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 109 109 5 109 6 1 1 23 41 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 110 110 6 110 5 1 1 22 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 34 ] 9 18 U A - - + MP 111 110 6 115 6 2 2 21 39 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -7.836 -7.795 -7.436 -3.794 -5.957 -7.798 2.220 -6.790 -7.445 1.323 -7.710 -5.649 3.103 -7.832 -3.590 -6.217 + ML 112 110 6 115 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 113 110 6 115 6 1 1 21 40 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 114 110 6 115 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 115 115 5 115 6 1 1 21 40 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 116 116 6 116 5 1 1 21 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 35 ] 10 17 C G - - + MP 117 116 6 121 6 2 2 19 37 -11.637 -11.577 -0.004 -10.353 -10.633 -11.028 -8.021 -8.050 -7.554 -4.088 -6.028 -7.856 3.184 -6.884 -7.587 0.019 -7.815 -5.994 2.506 -7.979 -3.679 -6.365 + ML 118 116 6 121 6 1 1 21 39 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 + MR 119 116 6 121 6 1 1 20 39 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 + D 120 116 6 121 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 + IL 121 121 5 121 6 1 1 20 39 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 + IR 122 122 6 122 5 1 1 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 + [ MATP 36 ] 11 16 U A - - + MP 123 122 6 127 4 2 2 17 35 -10.705 -10.912 -0.004 -9.326 -8.498 -8.756 -7.833 -4.969 -6.193 -7.989 1.976 -7.104 -7.931 -4.927 -8.060 -7.105 3.379 -8.342 0.623 -6.731 + ML 124 122 6 127 4 1 1 20 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 + MR 125 122 6 127 4 1 1 20 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 + D 126 122 6 127 4 0 0 19 37 -4.568 -4.250 -2.265 -0.520 + IL 127 127 5 127 4 1 1 22 40 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 + IR 128 128 6 128 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 37 ] 12 - U - - - + ML 129 128 6 131 3 1 1 14 32 -11.622 -0.002 -10.276 0.104 -1.394 -4.333 1.319 + D 130 128 6 131 3 0 0 16 34 -6.174 -1.687 -0.566 + IL 131 131 3 131 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 38 ] 13 - U - - - + ML 132 131 3 134 3 1 1 12 31 -11.622 -0.002 -10.276 -2.505 0.463 -5.033 1.272 + D 133 131 3 134 3 0 0 15 33 -6.174 -1.687 -0.566 + IL 134 134 3 134 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 39 ] 14 - U - - - + ML 135 134 3 137 3 1 1 11 29 -11.622 -0.002 -10.276 -7.616 -6.858 -8.607 1.994 + D 136 134 3 137 3 0 0 13 32 -6.174 -1.687 -0.566 + IL 137 137 3 137 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 + [ MATL 40 ] 15 - a - - - + ML 138 137 3 140 2 1 1 1 1 * 0.000 0.741 0.478 -2.313 -0.445 + D 139 137 3 140 2 0 0 0 0 * 0.000 + IL 140 140 3 140 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 + [ END 41 ] - - - - - - + E 141 140 3 -1 0 0 0 0 0 +// +HMMER3/f [3.3 | Nov 2019] +NAME Histone3 +ACC RF00032 +DESC Histone 3' UTR stem-loop +LENG 46 +MAXL 102 +ALPH RNA +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Fri Apr 4 13:03:46 2014 +COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED +NSEQ 46 +EFFN 42.133911 +CKSUM 471917655 +STATS LOCAL MSV -8.1088 0.74543 +STATS LOCAL VITERBI -8.5088 0.74543 +STATS LOCAL FORWARD -3.2029 0.74543 +HMM A C G U + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.16847 1.39084 1.71368 1.34673 + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 0.00000 * + 1 1.19718 0.92283 2.53752 1.50734 1 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 2 0.99976 0.91709 2.73454 1.78721 2 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 3 0.28707 2.15200 4.53977 2.09870 3 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 4 0.67303 1.40667 2.67938 1.73570 4 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 5 0.71631 0.93175 4.42267 2.24827 5 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 6 4.96323 6.10024 0.01150 6.11805 6 G - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 7 4.97477 6.07793 0.01151 6.10217 7 G - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 8 2.42219 0.35197 5.16373 1.59825 8 C - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 9 4.96709 1.22589 1.84282 0.61402 9 U - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 10 5.14332 0.56593 2.72176 1.02007 10 C - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 11 5.65512 1.39382 5.58556 0.29488 11 U - - < + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 12 1.31706 2.34288 4.27893 0.47454 12 U - - _ + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 13 3.10136 1.06700 4.79001 0.50640 13 U - - _ + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 14 6.52235 6.01860 7.19543 0.00466 14 U - - _ + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 15 0.87615 1.05939 2.96086 1.68645 15 a - - _ + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 16 0.43199 5.71946 1.06961 5.43487 16 A - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 17 1.03329 2.73783 0.55849 4.90865 17 G - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 18 0.62348 1.85123 1.21052 4.72873 18 A - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 19 1.62037 5.32794 0.34630 2.40773 19 G - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 20 6.16935 0.01425 6.02393 4.64210 20 C - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 21 6.22221 0.03904 6.06094 3.38213 21 C - - > + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 22 0.03027 3.82336 5.58493 5.47058 22 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 23 3.26053 0.29487 4.86483 1.56402 23 C - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 24 1.15929 0.76514 3.19669 1.71411 24 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.47612 0.97621 6.17794 0.01098 4.51736 1.09861 0.40547 + 25 0.90589 0.99871 2.78941 1.79574 26 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 26 0.37936 2.45545 2.76975 1.78857 27 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.03553 6.17794 3.41622 1.46634 0.26236 1.09861 0.40547 + 27 2.00288 0.98595 2.07379 1.00440 28 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00429 6.14670 6.14670 1.46634 0.26236 0.11900 2.18757 + 28 0.58277 2.57844 2.26067 1.34141 29 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 29 2.04103 1.64155 1.24300 0.94698 30 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.04224 6.17794 3.23682 1.46634 0.26236 1.09861 0.40547 + 30 0.90025 2.40010 2.48509 0.86868 31 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00432 6.14002 6.14002 1.46634 0.26236 0.10040 2.34838 + 31 1.14658 1.52988 1.97258 1.11897 32 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 32 0.99477 1.56394 2.34075 1.12508 33 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 33 1.30260 0.91111 1.74486 1.88763 34 c - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 34 0.81644 1.95418 2.55798 1.08218 35 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 35 0.88707 2.68494 1.54697 1.18084 36 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.02155 6.17794 3.95035 1.46634 0.26236 1.09861 0.40547 + 36 0.88692 1.97884 1.71659 1.30871 37 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00423 6.16062 6.16062 1.46634 0.26236 0.19522 1.72966 + 37 0.78649 1.68131 1.71782 1.72051 38 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 38 0.59588 2.08432 1.60986 2.08251 39 A - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 39 0.76886 1.58017 1.51684 2.19720 40 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.02859 6.17794 3.64554 1.46634 0.26236 1.09861 0.40547 + 40 0.91147 2.90974 1.18115 1.44117 41 a - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00426 6.15362 6.15362 1.46634 0.26236 0.14750 1.98676 + 41 1.19023 1.82584 1.84655 0.97555 42 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 42 1.35396 2.21010 1.23260 1.07716 43 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 43 1.25472 1.71330 1.50591 1.16232 44 u - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 44 1.37043 1.66018 2.98397 0.68259 45 U - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547 + 45 1.15612 1.70216 1.15511 1.67140 46 g - - : + 1.38629 1.38629 1.38629 1.38629 + 0.47997 6.17794 0.96989 1.46634 0.26236 1.09861 0.40547 + 46 2.25321 3.55314 1.66807 0.38906 47 U - - : + 1.38629 1.38629 1.38629 1.38629 + 0.00335 5.70132 * 1.46634 0.26236 0.00000 * +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_search.gtf Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,11 @@ +chr1 HAVANA gene 21 60 . + . gene_id "g1"; gene_type "protein_coding"; gene_name "GENE1"; +chr1 HAVANA transcript 21 60 . + . gene_id "g1"; transcript_id "g1_t1"; transcript_type "protein_coding"; gene_type "protein_coding"; transcript_name "g1_t1"; level 1; transcript_support_level "2"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA exon 21 60 . + . gene_id "g1"; transcript_id "g1_t1"; gene_type "protein_coding"; gene_name "GENE1"; transcript_type "protein_coding"; transcript_name "g1_t1-202"; exon_number 1; exon_id "g1_t1_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA CDS 31 44 . + . gene_id "g1"; transcript_id "g1_t1"; gene_type "protein_coding"; gene_name "GENE1"; transcript_type "protein_coding"; transcript_name "g1_t1-202"; exon_number 1; exon_id "g1_t1_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA transcript 21 60 . + . gene_id "g1"; transcript_id "g1_t2"; transcript_type "protein_coding"; gene_type "protein_coding"; transcript_name "g1_t2"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA exon 21 60 . + . gene_id "g1"; transcript_id "g1_t2"; gene_type "protein_coding"; gene_name "GENE1"; transcript_type "protein_coding"; transcript_name "g1_t2-202"; exon_number 1; exon_id "g1_t2_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA CDS 31 44 . + . gene_id "g1"; transcript_id "g1_t2"; gene_type "protein_coding"; gene_name "GENE1"; transcript_type "protein_coding"; transcript_name "g1_t2-202"; exon_number 1; exon_id "g1_t2_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA gene 21 60 . - . gene_id "g2"; gene_type "lncRNA"; gene_name "GENE2"; +chr1 HAVANA transcript 20 60 . - . gene_id "g2"; transcript_id "g2_t1"; transcript_type "lncRNA"; gene_type "lncRNA"; transcript_name "g2_t1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA exon 51 60 . - . gene_id "g2"; transcript_id "g2_t1"; gene_type "lncRNA"; gene_name "GENE1"; transcript_type "lncRNA"; transcript_name "g2_t1-202"; exon_number 1; exon_id "g2_t1_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA exon 21 40 . - . gene_id "g2"; transcript_id "g2_t1"; gene_type "lncRNA"; gene_name "GENE1"; transcript_type "lncRNA"; transcript_name "g2_t1-202"; exon_number 2; exon_id "g2_t1_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_search_gtf.region_annotations.tsv Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,2 @@ +region_id gene_id gene_name transcript_id region_annotation transcript_biotype +chr1:10-80(+) g1 GENE1 g1_t2 3'UTR protein_coding
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_table.txt Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,2 @@ +PUM1 mid1 did1 test1.bed +PUM2 mid2 did2 test2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rbp_ids.catrapid.omics.v2.1.human.6plus.txt Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,259 @@ +A1CF +ACIN1 +ACO1 +ADAR +AGGF1 +AGO1 +AGO2 +AKAP1 +AKAP8 +ANKHD1 +AUH +BCCIP +BOLL +BUD13 +CAPRIN1 +CBX7 +CDC40 +CELF1 +CELF2 +CELF4 +CELF5 +CELF6 +CNBP +CNOT4 +CPEB1 +CPEB2 +CPEB4 +CPSF6 +CPSF7 +CSTF2 +CSTF2T +DAZ3 +DAZAP1 +DDX3X +DDX6 +DDX19B +DDX24 +DDX54 +DDX55 +DDX58 +DDX59 +DGCR8 +DKC1 +EFTUD2 +EIF3D +EIF4A3 +EIF4B +EIF4G2 +ELAVL1 +ELAVL2 +ELAVL3 +ELAVL4 +ENOX1 +ERI1 +ESRP1 +ESRP2 +EWSR1 +FAM120A +FASTKD2 +FBL +FIP1L1 +FMR1 +FTO +FUBP1 +FUBP3 +FUS +FXR1 +FXR2 +G3BP1 +G3BP2 +GNL3 +GPKOW +GRSF1 +GRWD1 +GTF2F1 +HLTF +HNRNPA0 +HNRNPA1 +HNRNPA1L2 +HNRNPA2B1 +HNRNPA3 +HNRNPAB +HNRNPC +HNRNPCL1 +HNRNPD +HNRNPDL +HNRNPF +HNRNPH1 +HNRNPH2 +HNRNPK +HNRNPL +HNRNPLL +HNRNPM +HNRNPU +HNRNPUL1 +IFIH1 +IGF2BP1 +IGF2BP2 +IGF2BP3 +IGHMBP2 +ILF2 +ILF3 +KHDRBS1 +KHDRBS2 +KHDRBS3 +KHSRP +LARP4 +LARP4B +LIN28A +LIN28B +LSM11 +MATR3 +MBNL1 +METAP2 +MSI1 +MSI2 +MTPAP +NCBP2 +NELFE +NKRF +NOL12 +NONO +NOP56 +NOP58 +NOVA1 +NOVA2 +NPM1 +NSUN2 +NUMA1 +NUP42 +NXF1 +OAS1 +OBI1 +PABPC1 +PABPC3 +PABPC4 +PABPC5 +PABPN1 +PABPN1L +PARP1 +PCBP1 +PCBP2 +PCBP4 +PPIE +PPIG +PPIL4 +PPRC1 +PRPF8 +PRR3 +PTBP1 +PTBP2 +PTBP3 +PUF60 +PUM1 +PUM2 +QKI +RALY +RALYL +RANGAP1 +RBFOX1 +RBFOX2 +RBFOX3 +RBM3 +RBM4 +RBM4B +RBM5 +RBM6 +RBM8A +RBM10 +RBM14 +RBM15 +RBM15B +RBM22 +RBM23 +RBM24 +RBM25 +RBM28 +RBM39 +RBM41 +RBM42 +RBM45 +RBM46 +RBM47 +RBMS1 +RBMS2 +RBMS3 +RBMX +RBMY1A1 +RC3H1 +TROVE2 +RPS5 +SAFB2 +SAMD4A +SART3 +SF1 +SF3A3 +SF3B4 +SFPQ +SLTM +SMNDC1 +SND1 +SNRNP70 +SNRPA +SNRPB2 +SOX2 +SRP14 +SRP68 +SRRM4 +SRSF1 +SRSF2 +SRSF3 +SRSF4 +SRSF5 +SRSF6 +SRSF7 +SRSF8 +SRSF9 +SRSF10 +SRSF11 +SSB +SUB1 +SUGP2 +SUPV3L1 +SYNCRIP +TAF15 +TARBP2 +TARDBP +TBRG4 +TIA1 +TIAL1 +TNRC6A +TRA2A +TRA2B +TRNAU1AP +TUT1 +U2AF1 +U2AF2 +UCHL5 +UNK +UPF1 +WDR33 +XPO5 +XRCC6 +XRN2 +YBX1 +YBX2 +YBX3 +YTHDC1 +YWHAG +ZC3H10 +ZCRB1 +ZFP36 +ZFP36L2 +ZNF184 +ZNF326 +ZNF622 +ZNF638 +ZRANB2 +SLBP
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of built-in genome --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> + <!-- IDs table file --> + <table name="rbp_ids_table" comment_char="#"> + <columns>value</columns> + <file path="${__HERE__}/tool-data/rbp_ids.catrapid.omics.v2.1.human.6plus.txt" /> + </table> +</tables> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sun Dec 03 12:51:54 2023 +0000 @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of built-in genome --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> + <!-- IDs table file --> + <table name="rbp_ids_table" comment_char="#"> + <columns>value</columns> + <file path="${__HERE__}/tool-data/rbp_ids.catrapid.omics.v2.1.human.6plus.txt" /> + </table> +</tables> \ No newline at end of file