annotate defuse.xml @ 1:36306d8086fa

Remove defuse dir
author Jim Johnson <jj@umn.edu>
date Fri, 16 Sep 2011 12:41:37 -0500
parents
children 4245c2b047de
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
1 <tool id="defuse" name="DeFuse" version="1.0">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 <description>identify fusion transcripts</description>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
3 <requirements>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 <requirement type="binary"></requirement>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
5 </requirements>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
6 <command interpreter="perl">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
7 scripts/defuse.pl
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
8 -c `cp $defuse_config $config_txt; echo $defuse_config`
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 -d `mkdir -p data_dir; ln -s $left_pairendreads data_dir/reads_1.fastq; ln -s $right_pairendreads data_dir/reads_2.fastq; echo data_dir`
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 -o output_dir -p 8
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 </command>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 <inputs>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
13 <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads. (FASTQ interlacer will pair reads and remove the unpaired. FASTQ de-interlacer will separate the result into left and right reads.)"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
15 <conditional name="refGenomeSource">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
18 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
19 </param>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 <when value="indexed">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 <param name="index" type="select" label="Select a Reference Dataset" help="if your genome of interest is not listed - contact Galaxy team">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22 <options from_file="defuse.loc">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
23 <column name="name" index="1"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 <column name="value" index="2"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
25 <filter type="sort_by" column="0" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
26 <validator type="no_options" message="No indexes are available" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 </options>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
28 </param>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
29 <conditional name="defuse_param">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
30 <param name="settings" type="select" label="Defuse parameter settings" help="">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
31 <option value="preSet">Default settings</option>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
32 <option value="full">Full parameter list</option>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
33 </param>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
34 <when value="preSet" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
35 <when value="full">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
36 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
37 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
38 <param name="discord_read_trim" type="integer" value="50" optional="true" label="Trim length for discordant reads discord_read_trim" help="(split reads are not trimmed)" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
39 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
40 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
41 </param>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
42 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
43 <param name="split_count_threshold" type="integer" value="3" optional="true" label="Filter split_count_threshold" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
44 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
45 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
46 </param>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
47 <param name="max_dist_pos" type="integer" value="600" optional="true" label="Filter max_dist_pos" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
48 <param name="num_dist_genes" type="integer" value="500" optional="true" label="Filter num_dist_genes" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
49 <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
50 <param name="max_concordant_ratio" type="float" value="0.1" optional="true" label="Filter max_concordant_ratio">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
51 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
52 </param>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
53 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" />
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
54 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
55 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
56 </param>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
57 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
58 <help>Position density when calculating covariance</help>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
59 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
60 </param>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
61 <param name="denovo_assembly" type="select" label="denovo_assembly" help="">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
62 <option value="">Use Default</option>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
63 <option value="no">no</option>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
64 <option value="yes">yes</option>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
65 </param>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
66 <!--
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
67 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
68 -->
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
69 </when> <!-- full -->
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
70 </conditional> <!-- defuse_param -->
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
71 </when>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
72 <when value="history">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
73 <param name="config" type="data" format="txt" label="Defuse Config file" help=""/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
74 </when> <!-- history -->
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
75 </conditional> <!-- refGenomeSource -->
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
76 </inputs>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
77 <configfiles>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
78 <configfile name="defuse_config">
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
79 #import ast
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
80 #if $refGenomeSource.genomeSource == "history":
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
81 #include raw $refGenomeSource.config.__str__
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
82 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
83 #set $ref_dict = dict($ast.literal_eval($refGenomeSource.index.value))
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
84 #
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
85 # Configuration file for defuse
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
86 #
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
87 # At a minimum, change all values enclused by []
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
88 #
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
89 # Gene/Transcript id pattern
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
90 gene_id_pattern = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
91 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
92 $ref_dict['gene_id_pattern']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
93 transcript_id_pattern = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
94 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
95 ENSG\d+
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
96 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
97 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
98 $ref_dict['transcript_id_pattern']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
99 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
100 ENST\d+
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
101 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
102
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
103 # Directory where the defuse code was unpacked
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
104 ## Default location in the tool/defuse directory
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
105 # source_directory = ${__root_dir__}/tools/defuse
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
106 source_directory = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
107 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
108 $ref_dict['source_directory']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
109 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
110 ${__root_dir__}/tools/defuse
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
111 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
112
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
113 # Directory where you want your dataset
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
114 dataset_directory = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
115 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
116 $ref_dict['dataset_directory']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
117 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
118 /project/db/genomes/Hsapiens/hg19/defuse
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
119 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
120
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
121 # Input genome and gene models
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
122 gene_models = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
123 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
124 $ref_dict['gene_models']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
125 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
126 \$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
127 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
128 genome_fasta = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
129 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
130 $ref_dict['genome_fasta']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
131 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
132 \$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
133 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
134
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
135 # Repeat table from ucsc genome browser
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
136 repeats_filename = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
137 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
138 $ref_dict['repeats_filename']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
139 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
140 \$(dataset_directory)/rmsk.txt
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
141 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
142
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
143 # EST info downloaded from ucsc genome browser
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
144 est_fasta = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
145 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
146 $ref_dict['est_fasta']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
147 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
148 \$(dataset_directory)/est.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
149 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
150 est_alignments = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
151 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
152 $ref_dict['est_alignments']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
153 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
154 \$(dataset_directory)/intronEst.txt
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
155 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
156
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
157 # Unigene clusters downloaded from ncbi
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
158 unigene_fasta = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
159 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
160 $ref_dict['unigene_fasta']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
161 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
162 \$(dataset_directory)/Hs.seq.uniq
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
163 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
164
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
165 # Paths to external tools
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
166 bowtie_bin = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
167 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
168 $ref_dict['bowtie_bin']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
169 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
170 /soft/bowtie/0.12.7/bowtie
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
171 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
172 bowtie_build_bin = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
173 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
174 $ref_dict['bowtie_build_bin']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
175 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
176 /soft/bowtie/0.12.7/bowtie-build
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
177 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
178 blat_bin = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
179 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
180 $ref_dict['blat_bin']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
181 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
182 /soft/blat/34/bin/blat
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
183 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
184 fatotwobit_bin = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
185 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
186 $ref_dict['fatotwobit_bin']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
187 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
188 /soft/blat/34/bin/faToTwoBit
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
189 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
190 r_bin = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
191 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
192 $ref_dict['r_bin']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
193 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
194 /project/sdml-sles11-weblocal/R-2.12.1/bin/R
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
195 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
196 rscript_bin = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
197 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
198 $ref_dict['rscript_bin']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
199 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
200 /project/sdml-sles11-weblocal/R-2.12.1/bin/Rscript
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
201 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
202
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
203 #raw
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
204 # Dataset files
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
205 dataset_prefix = $(dataset_directory)/defuse
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
206 chromosome_prefix = $(dataset_prefix).dna.chromosomes
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
207 exons_fasta = $(dataset_prefix).exons.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
208 cds_fasta = $(dataset_prefix).cds.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
209 cdna_regions = $(dataset_prefix).cdna.regions
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
210 cdna_fasta = $(dataset_prefix).cdna.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
211 reference_fasta = $(dataset_prefix).reference.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
212 rrna_fasta = $(dataset_prefix).rrna.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
213 ig_gene_list = $(dataset_prefix).ig.gene.list
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
214 repeats_regions = $(dataset_directory)/repeats.regions
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
215 est_split_fasta1 = $(dataset_directory)/est.1.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
216 est_split_fasta2 = $(dataset_directory)/est.2.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
217 est_split_fasta3 = $(dataset_directory)/est.3.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
218 est_split_fasta4 = $(dataset_directory)/est.4.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
219 est_split_fasta5 = $(dataset_directory)/est.5.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
220 est_split_fasta6 = $(dataset_directory)/est.6.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
221 est_split_fasta7 = $(dataset_directory)/est.7.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
222 est_split_fasta8 = $(dataset_directory)/est.8.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
223 est_split_fasta9 = $(dataset_directory)/est.9.fa
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
224
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
225 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
226 prefilter1 = $(unigene_fasta)
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
227
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
228 # deFuse scripts and tools
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
229 scripts_directory = $(source_directory)/scripts
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
230 tools_directory = $(source_directory)/tools
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
231 data_directory = $(source_directory)/data
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
232 #end raw
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
233
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
234 # Path to samtools, 0.1.8 is compiled for you, use other versions at your own risk
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
235 samtools_bin = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
236 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
237 $ref_dict['samtools_bin']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
238 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
239 \$(source_directory)/external/samtools-0.1.8/samtools
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
240 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
241
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
242 # Bowtie parameters
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
243 bowtie_threads = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
244 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
245 $ref_dict['bowtie_threads']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
246 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
247 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
248 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
249 bowtie_quals = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
250 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
251 $ref_dict['bowtie_quals']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
252 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
253 --phred33-quals
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
254 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
255 max_insert_size = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
256 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_insert_size.__str__ != "":
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
257 $refGenomeSource.defuse_param.max_insert_size
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
258 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
259 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
260 $ref_dict['max_insert_size']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
261 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
262 500
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
263 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
264 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
265
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
266 # Parameters for building the dataset
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
267 chromosomes = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
268 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
269 $ref_dict.chromosomes
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
270 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
271 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
272 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
273 mt_chromosome = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
274 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
275 $ref_dict['mt_chromosome']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
276 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
277 MT
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
278 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
279 gene_sources = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
280 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
281 $ref_dict['gene_sources']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
282 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
283 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
284 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
285 ig_gene_sources = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
286 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
287 $ref_dict['ig_gene_sources']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
288 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
289 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
290 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
291 rrna_gene_sources = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
292 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
293 $ref_dict['rrna_gene_sources']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
294 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
295 Mt_rRNA,rRNA,rRNA_pseudogene
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
296 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
297
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
298 # Blat sequences per job
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
299 num_blat_sequences = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
300 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
301 $ref_dict['num_blat_sequences']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
302 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
303 10000
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
304 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
305
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
306 # Minimum gene fusion range
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
307 dna_concordant_length = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
308 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.dna_concordant_length.__str__ != "":
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
309 $refGenomeSource.defuse_param.dna_concordant_length
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
310 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
311 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
312 $ref_dict['dna_concordant_length']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
313 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
314 2000
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
315 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
316 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
317
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
318 # Trim length for discordant reads (split reads are not trimmed)
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
319 discord_read_trim = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
320 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.discord_read_trim.__str__ != "":
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
321 $refGenomeSource.defuse_param.discord_read_trim
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
322 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
323 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
324 $ref_dict['discord_read_trim']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
325 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
326 50
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
327 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
328 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
329
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
330 # Filtering parameters
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
331 clustering_precision = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
332 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.clustering_precision.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
333 $refGenomeSource.defuse_param.clustering_precision
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
334 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
335 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
336 $ref_dict['clustering_precision']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
337 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
338 0.95
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
339 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
340 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
341 span_count_threshold = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
342 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.span_count_threshold.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
343 $refGenomeSource.defuse_param.span_count_threshold
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
344 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
345 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
346 $ref_dict['span_count_threshold']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
347 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
348 5
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
349 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
350 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
351 split_count_threshold = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
352 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_count_threshold.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
353 $refGenomeSource.defuse_param.split_count_threshold
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
354 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
355 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
356 $ref_dict['split_count_threshold']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
357 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
358 3
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
359 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
360 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
361 percent_identity_threshold = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
362 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.percent_identity_threshold.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
363 $refGenomeSource.defuse_param.percent_identity_threshold
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
364 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
365 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
366 $ref_dict['percent_identity_threshold']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
367 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
368 0.90
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
369 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
370 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
371 max_dist_pos = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
372 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_dist_pos.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
373 $refGenomeSource.defuse_param.max_dist_pos
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
374 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
375 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
376 $ref_dict['max_dist_pos']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
377 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
378 600
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
379 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
380 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
381 num_dist_genes = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
382 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.num_dist_genes.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
383 $refGenomeSource.defuse_param.num_dist_genes
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
384 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
385 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
386 $ref_dict['num_dist_genes']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
387 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
388 500
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
389 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
390 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
391 split_min_anchor = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
392 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_min_anchor.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
393 $refGenomeSource.defuse_param.split_min_anchor
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
394 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
395 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
396 $ref_dict['split_min_anchor']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
397 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
398 4
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
399 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
400 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
401 max_concordant_ratio = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
402 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_concordant_ratio.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
403 $refGenomeSource.defuse_param.max_concordant_ratio
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
404 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
405 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
406 $ref_dict['max_concordant_ratio']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
407 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
408 0.1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
409 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
410 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
411 splice_bias = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
412 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.splice_bias.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
413 $refGenomeSource.defuse_param.splice_bias
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
414 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
415 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
416 $ref_dict['splice_bias']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
417 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
418 10
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
419 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
420 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
421 denovo_assembly = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
422 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.denovo_assembly.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
423 $refGenomeSource.defuse_param.denovo_assembly
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
424 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
425 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
426 $ref_dict['denovo_assembly']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
427 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
428 no
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
429 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
430 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
431 probability_threshold = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
432 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.probability_threshold.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
433 $refGenomeSource.defuse_param.probability_threshold
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
434 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
435 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
436 $ref_dict['probability_threshold']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
437 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
438 0.50
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
439 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
440 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
441 positive_controls = \$(data_directory)/controls.txt
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
442
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
443 # Position density when calculating covariance
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
444 covariance_sampling_density = #slurp
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
445 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.covariance_sampling_density.__str__ != ""
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
446 $refGenomeSource.defuse_param.covariance_sampling_density
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
447 #else
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
448 #try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
449 $ref_dict['covariance_sampling_density']
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
450 #except
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
451 0.01
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
452 #end try
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
453 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
454
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
455
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
456 # Number of reads for each job in split
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
457 reads_per_job = 1000000
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
458
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
459 # Number of regions for each breakpoint sequence job in split
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
460 regions_per_job = 20
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
461
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
462 #raw
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
463 # If you have command line 'mail' and wish to be notified
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
464 # mailto = andrew.mcpherson@gmail.com
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
465
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
466 # Remove temp files
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
467 remove_job_files = yes
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
468 remove_job_temp_files = yes
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
469
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
470 # Converting to fastq
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
471 # Fastq converter config format 1 for reads stored in separate files for each end
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
472 # data_lane_rexex_N is a perl regex which stores the lane id in $1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
473 # data_end_regex_N is a perl regex which stores the end, 1 or 2, in $1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
474 # data_compress_regex_N is a perl regex which stores the compression extension in $1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
475 # data_convert_N is the associated conversion utility that takes data at stdin and outputs fastq at stdout
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
476 # Fastq converter config format 2 for reads stored in separate files for each end
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
477 # data_lane_regex_N is a perl regex which stores the lane id in $1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
478 # data_compress_regex_N is a perl regex which stores the compression extension in $1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
479 # data_end1_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 1 at stdout
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
480 # data_end2_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 2 at stdout
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
481
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
482 data_lane_regex_1 = ^(.+)_[12]_export\.txt.*$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
483 data_end_regex_1 = ^.+_([12])_export\.txt.*$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
484 data_compress_regex_1 = ^.+_[12]_export\.txt(.*)$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
485 data_converter_1 = $(scripts_directory)/fq_all2std.pl export2std
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
486
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
487 data_lane_regex_2 = ^(.+)_[12]_concat_qseq\.txt.*$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
488 data_end_regex_2 = ^.+_([12])_concat_qseq\.txt.*$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
489 data_compress_regex_2 = ^.+_[12]_concat_qseq\.txt(.*)$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
490 data_converter_2 = $(scripts_directory)/qseq2fastq.pl
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
491
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
492 data_lane_regex_3 = ^(.+)\.bam.*$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
493 data_compress_regex_3 = ^.+\.bam(.*)$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
494 data_end1_converter_3 = samtools view - | filter_sam_mate.pl 1 | sam_to_fastq.pl
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
495 data_end2_converter_3 = samtools view - | filter_sam_mate.pl 2 | sam_to_fastq.pl
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
496
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
497 data_lane_regex_4 = ^(.+).[12].fastq.*$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
498 data_end_regex_4 = ^.+.([12]).fastq.*$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
499 data_compress_regex_4 = ^.+.[12].fastq(.*)$
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
500 data_converter_4 = cat
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
501 #end raw
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
502
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
503 #end if
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
504
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
505 </configfile>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
506 </configfiles>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
507 <outputs>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
508 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
509 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" from_work_dir="output_dir/log/defuse.log"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
510 <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" from_work_dir="output_dir/results.tsv"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
511 <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" from_work_dir="output_dir/results.filtered.tsv"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
512 <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" from_work_dir="output_dir/results.classify.tsv"/>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
513 </outputs>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
514 <tests>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
515 </tests>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
516 <help>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
517 **DeFuse**
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
518
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
519 DeFuse_ is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion.
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
520
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
521 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
522
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
523 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
524
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
525 ------
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
526
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
527 **Inputs**
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
528
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
529 DeFuse requires 2 fastq files for paried reads, one with the left mate of the paired reads, and a second fastq with the the right mate of the paired reads (**with reads in the same order as in the first fastq dataset**).
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
530
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
531 If your fastq files have reads in different orders or include unpaired reads, you can preprocess them with **FASTQ interlacer** to create a single interlaced fastq dataset with only the paired reads and input that to **FASTQ de-interlacer** to separate the reads into a left fastq and right fastq.
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
532
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
533 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.4_:
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
534 - genome_fasta from Ensembl
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
535 - gene_models from Ensembl
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
536 - repeats_filename from UCSC RepeatMasker rmsk.txt
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
537 - est_fasta from UCSC
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
538 - est_alignments from UCSC intronEst.txt
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
539 - unigene_fasta from NCBI
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
540
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
541 .. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
542
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
543 ------
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
544
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
545 **Outputs**
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
546
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
547 The galaxy history will contain 5 outputs: the config.txt file that provides DeFuse with its parameters, the defuse.log which details what DeFuse has done and can be useful in determining any errors, and the 3 results files that defuse generates.
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
548
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
549 DeFuse generates 3 results files: results.txt, results.filtered.txt, and results.classify.txt. All three files have the same format, though results.classify.txt has a probability column from the application of the classifier to results.txt, and results.filtered.txt has been filtered according to the threshold probability as set in config.txt.
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
550
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
551 The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order):
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
552
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
553 - **Identification**
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
554 - cluster_id : random identifier assigned to each prediction
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
555 - library_name : library name given on the command line of defuse
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
556 - gene1 : ensembl id of gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
557 - gene2 : ensembl id of gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
558 - gene_name1 : name of gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
559 - gene_name2 : name of gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
560 - **Evidence**
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
561 - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
562 - concordant_ratio : proportion of spanning reads considered concordant by blat
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
563 - denovo_min_count : minimum kmer count across denovo assembled sequence
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
564 - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
565 - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
566 - gene_align_strand1 : alignment strand for spanning read alignments to gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
567 - gene_align_strand2 : alignment strand for spanning read alignments to gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
568 - min_map_count : minimum of the number of genomic mappings for each spanning read
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
569 - max_map_count : maximum of the number of genomic mappings for each spanning read
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
570 - mean_map_count : average of the number of genomic mappings for each spanning read
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
571 - num_multi_map : number of spanning reads that map to more than one genomic location
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
572 - span_count : number of spanning reads supporting the fusion
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
573 - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
574 - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
575 - span_coverage_min : minimum of span_coverage1 and span_coverage2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
576 - span_coverage_max : maximum of span_coverage1 and span_coverage2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
577 - splitr_count : number of split reads supporting the prediction
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
578 - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
579 - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
580 - splitr_sequence : fusion sequence predicted by split reads
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
581 - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
582 - **Annotation**
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
583 - adjacent : fusion between adjacent genes
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
584 - altsplice : fusion likely the product of alternative splicing between adjacent genes
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
585 - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
586 - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
587 - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
588 - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
589 - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
590 - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
591 - deletion : fusion produced by a genomic deletion
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
592 - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
593 - eversion : fusion produced by a genomic eversion
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
594 - exonboundaries : fusion splice at exon boundaries
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
595 - expression1 : expression of gene 1 as number of concordant pairs aligned to exons
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
596 - expression2 : expression of gene 2 as number of concordant pairs aligned to exons
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
597 - gene_chromosome1 : chromosome of gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
598 - gene_chromosome2 : chromosome of gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
599 - gene_end1 : end position for gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
600 - gene_end2 : end position for gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
601 - gene_location1 : location of breakpoint in gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
602 - gene_location2 : location of breakpoint in gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
603 - gene_start1 : start of gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
604 - gene_start2 : start of gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
605 - gene_strand1 : strand of gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
606 - gene_strand2 : strand of gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
607 - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
608 - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
609 - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
610 - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
611 - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
612 - interchromosomal : fusion produced by an interchromosomal translocation
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
613 - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
614 - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
615 - inversion : fusion produced by genomic inversion
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
616 - orf : fusion combines genes in a way that preserves a reading frame
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
617 - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt)
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
618 - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
619 - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
620 - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
621 - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
622 - splice_score : number of nucleotides similar to GTAG at fusion splice
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
623 - num_splice_variants : number of potential splice variants for this gene pair
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
624 - splicing_index1 : number of concordant pairs in gene 1 spanning the fusion splice / breakpoint, divided by number of spanning reads supporting the fusion with gene 2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
625 - splicing_index2 : number of concordant pairs in gene 2 spanning the fusion splice / breakpoint, divided by number of spanning reads supporting the fusion with gene 1
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
626
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
627
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
628 **Example**
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
629
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
630 results.tsv::
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
631
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
632 cluster_id splitr_sequence splitr_count splitr_span_pvalue splitr_pos_pvalue splitr_min_pvalue adjacent altsplice break_adj_entropy1 break_adj_entropy2 break_adj_entropy_min break_predict breakpoint_homology breakseqs_estislands_percident cdna_breakseqs_percident concordant_ratio deletion est_breakseqs_percident eversion exonboundaries expression1 expression2 gene1 gene2 gene_align_strand1 gene_align_strand2 gene_chromosome1 gene_chromosome2 gene_end1 gene_end2 gene_location1 gene_location2 gene_name1 gene_name2 gene_start1 gene_start2 gene_strand1 gene_strand2 genome_breakseqs_percident genomic_break_pos1 genomic_break_pos2 genomic_strand1 genomic_strand2 interchromosomal interrupted_index1 interrupted_index2 inversion library_name max_map_count max_repeat_proportion mean_map_count min_map_count num_multi_map num_splice_variants orf read_through repeat_proportion1 repeat_proportion2 span_count span_coverage1 span_coverage2 span_coverage_max span_coverage_min splice_score splicing_index1 splicing_index2
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
633 1169 GCTTACTGTATGCCAGGCCCCAGAGGGGCAACCACCCTCTAAAGAGAGCGGCTCCTGCCTCCCAGAAAGCTCACAGACTGTGGGAGGGAAACAGGCAGCAGGTGAAGATGCCAAATGCCAGGATATCTGCCCTGTCCTTGCTTGATGCAGCTGCTGGCTCCCACGTTCTCCCCAGAATCCCCTCACACTCCTGCTGTTTTCTCTGCAGGTTGGCAGAGCCCCATGAGGGCAGGGCAGCCACTTTGTTCTTGGGCGGCAAACCTCCCTGGGCGGCACGGAAACCACGGTGAGAAGGGGGCAGGTCGGGCACGTGCAGGGACCACGCTGCAGG|TGTACCCAACAGCTCCGAAGAGACAGCGACCATCGAGAACGGGCCATGATGACGATGGCGGTTTTGTCGAAAAGAAAAGGGGGAAATGTGGGGAAAAGCAAGAGAGATCAGATTGTTACTGTGTCTGTGTAGAAAGAAGTAGACATGGGAGACTCCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGAGATTCGGTGACCCCACCCCCAACCCCGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTGAATGGATTAAGGGCGGTGCGAGACGTGCTTT 2 0.000436307890680442 0.110748295953850 0.0880671602973091 N Y 3.19872427442695 3.48337348351473 3.19872427442695 splitr 0 0 0 0 Y 0 N N 0 0 ENSG00000105549 ENSG00000213753 + - 19 19 376013 59111168 intron upstream THEG AC016629.2 361750 59084870 - + 0 375099 386594 + - N 8.34107429512245 - N output_dir 82 0.677852348993289 40.6666666666667 1 11 1 N N 0.361271676300578 0.677852348993289 12 0.758602776578432 0.569678713445872 0.758602776578432 0.569678713445872 2 0.416666666666667 -
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
634 3596 TGGGGGTTGAGGCTTCTGTTCCCAGGTTCCATGACCTCAGAGGTGGCTGGTGAGGTTATGACCTTTGCCCTCCAGCCCTGGCTTAAAACCTCAGCCCTAGGACCTGGTTAAAGGAAGGGGAGATGGAGCTTTGCCCCGACCCCCCCCCGTTCCCCTCACCTGTCAGCCCGAGCTGGGCCAGGGCCCCTAGGTGGGGAACTGGGCCGGGGGGCGGGCACAAGCGGAGGTGGTGCCCCCAAAAGGGCTCCCGGTGGGGTCTTGCTGAGAAGGTGAGGGGTTCCCGGGGCCGCAGCAGGTGGTGGTGGAGGAGCCAAGCGGCTGTAGAGCAAGGGGTGAGCAGGTTCCAGACCGTAGAGGCGGGCAGCGGCCACGGCCCCGGGTCCAGTTAGCTCCTCACCCGCCTCATAGAAGCGGGGTGGCCTTGCCAGGCGTGGGGGTGCTGCC|TTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCAGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGCCCCCCGGCCGGGGCCGGAGAGGGGCTGACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCGCGAAGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACTGATTTAATGAGCCATTCGCAGTTTCACTGTACCGGCCGTGCGTACTTAGACATGCATGGCTTAATCTTTGAGACAAGCATATGCTACTGGCAGG 250 7.00711162298275e-72 0.00912124762512338 0.00684237452309549 N N 3.31745197152461 3.47233119514066 3.31745197152461 splitr 7 0.0157657657657656 0 0 N 0.0135135135135136 N N 0 0 ENSG00000156860 ENSG00000212932 - + 16 21 30682131 48111157 coding upstream FBRS RPL23AP4 30670289 48110676 + + 0.0157657657657656 30680678 9827473 - + Y - - N output_dir 2 1 1.11111111111111 1 1 1 N N 0 1 9 0.325530693397641 0.296465452915709 0.325530693397641 0.296465452915709 2 - -
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
635
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
636 </help>
36306d8086fa Remove defuse dir
Jim Johnson <jj@umn.edu>
parents:
diff changeset
637 </tool>