Mercurial > repos > iuc > qualimap_bamqc
changeset 0:ac607906f10a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_bamqc.xml Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,474 @@ +<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@"> + <macros> + <import>qualimap_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + #import os + @SET_JAVA_OPTS@ && + + ## Set some default file names and paths + ## where we expect tool output to end up. + ## Note that most of these need to be overwritten if the user is + ## interested in regions *outside* those defined in a custom regions + ## file. + #set $out_dir = 'results' + #set $report_name = 'qualimapReport' + #set $summary_report = 'genome_results.txt' + #set $coverage_file = os.path.join($out_dir, 'coverage.txt') + ## This is the only file path that qualimap does not calculate + ## from $out_dir. + #set $per_base_coverage_target = $coverage_file + + qualimap bamqc + -bam '$input1' -outdir results -outformat html + --collect-overlap-pairs + #if str($stats_regions.region_select) == 'custom_regions': + -gff ${stats_regions.regions} + #if $stats_regions.outside_stats: + #set $report_name = 'qualimapReportOutsideRegions' + #set $summary_report = 'outside_results.txt' + #set $coverage_file = os.path.join( + $out_dir, 'outside_coverage.txt' + ) + #if $per_base_coverage: + #set $per_base_coverage_target = '/dev/null' + #end if + ${stats_regions.outside_stats} + #end if + #end if + #if $per_base_coverage: + $per_base_coverage $per_base_coverage_target + #end if + -nw ${plot_specific.n_bins} + ${plot_specific.paint_chromosome_limits} + #if $plot_specific.genome_gc_distr: + --genome-gc-distr ${plot_specific.genome_gc_distr} + #end if + -hm ${plot_specific.homopolymer_size} + + #if $duplicate_skipping: + --skip-duplicated + #if str($duplicate_skipping) == '0,1': + --skip-dup-mode 2 + #else: + --skip-dup-mode ${duplicate_skipping} + #end if + #end if + -nt \${GALAXY_SLOTS:-1} && + + #if $per_base_coverage: + mv $coverage_file '$output_per_base_coverage' && + #end if + @MASSAGE_OUTPUT@ + ]]></command> + <inputs> + <param argument="-bam" name="input1" type="data" format="bam" + label="Mapped reads input dataset" /> + <conditional name="stats_regions"> + <param name="region_select" type="select" label="Reference genome regions to calculate mapping statistics for"> + <option value="all">All (whole genome)</option> + <option value="custom_regions">Select regions</option> + </param> + <when value="all" /> + <when value="custom_regions"> + <param argument="-gff" name="regions" type="data" format="gff,gtf,bed" + label="Dataset specifying regions" /> + <param argument="-os" name="outside_stats" type="boolean" truevalue="--outside-stats" falsevalue="" checked="false" + label="Invert regions" + help="If selected, report read statistics *outside* the regions in the regions file." /> + </when> + </conditional> + <param argument="-oc" name="per_base_coverage" type="boolean" truevalue="--output-genome-coverage" falsevalue="" checked="false" + label="Generate per-base coverage output" + help="Produce additional tabular output listing the coverage at every site (omitting only zero-coverage positions) in the selected regions of the genome. Caution: Will generate a huge dataset for anything but small input genomes or restricted regions!" /> + <param argument="--skip-dup-mode" name="duplicate_skipping" type="select" display="checkboxes" multiple="true" optional="true" + label="Skip duplicate reads"> + <option value="0" selected="true">Reads flagged as duplicates in input</option> + <option value="1">Duplicates detected by Qualimap</option> + </param> + <section name="plot_specific" title="Settings affecting specific plots" expanded="false"> + <param argument="-nw" name="n_bins" type="integer" value="400" + label="Number of bins to use in across-reference plots" + help="Affected plots: Coverage, Mapping Quality and Insert Size across reference, Mapped reads GC-content distribution; the value determines the resolution of the affected plots. Note: The lower the value, the higher the memory usage of the tool!" /> + <param argument="-c" name="paint_chromosome_limits" type="boolean" truevalue="--paint-chromosome-limits" falsevalue="" checked="true" + label="Draw chromosome limits" + help="Affected plots: Coverage, Mapping Quality and Insert Size across reference; in across-reference plots, indicate chromosome boundaries with dotted lines and labels" /> + <param argument="-gd" name="genome_gc_distr" type="select" optional="true" + label="Plot expected GC-content distribution of the following reference genome" + help="Affected plot: Mapped reads GC-content distribution; include a precalculated GC-content distribution for the selected (Qualimap-supported) reference genome in the plot"> + <option value="hg19">Human genome (hg19)</option> + <option value="mm9">Mouse genome (mm9)</option> + <option value="mm10">Mouse genome (mm10)</option> + </param> + <param argument="-hm" name="homopolymer_size" type="integer" value="3" min="2" + label="Homopolymer size" + help="Affected plot: Homopolymer indels; sets the minimal number of consecutive bases that define a homopolymer" /> + </section> + </inputs> + <outputs> + <data name="output_html" format="html" + label="${tool.name} report on ${on_string}" /> + <data name="output_per_base_coverage" format="tsv" + label="${tool.name} per-base coverage on ${on_string}"> + <filter>per_base_coverage</filter> + </data> + <collection name="raw_data" type="list" + label="Raw data for ${tool.name} on ${on_string}"> + <data name="genome_results" format="txt" from_work_dir="results/summary_report.txt" /> + <data name="coverage_across_reference" format="tsv" from_work_dir="results/coverage_across_reference.txt" /> + <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" /> + <data name="genome_fraction_coverage" format="tsv" from_work_dir="results/genome_fraction_coverage.txt" /> + <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" /> + <data name="mapped_reads_clipping_profile" format="tsv" from_work_dir="results/mapped_reads_clipping_profile.txt" /> + <data name="mapped_reads_gc-content_distribution" format="tsv" from_work_dir="results/mapped_reads_gc-content_distribution.txt" /> + <data name="mapped_reads_nucleotide_content" format="tsv" from_work_dir="results/mapped_reads_nucleotide_content.txt" /> + <data name="mapping_quality_across_reference" format="tsv" from_work_dir="results/mapping_quality_across_reference.txt" /> + <data name="mapping_quality_histogram" format="tsv" from_work_dir="results/mapping_quality_histogram.txt" /> + </collection> + </outputs> + <tests> + <test expect_num_outputs="12"> + <param name="input1" value="test_mapped_reads.bam"/> + <output name="output_html" ftype="html"> + <assert_contents> + <has_text text="Qualimap report: BAM QC" /> + </assert_contents> + </output> + <output_collection name="raw_data" type="list"> + <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" /> + </output_collection> + </test> + <test expect_num_outputs="13"> + <param name="input1" value="test_mapped_reads.bam" /> + <param name="per_base_coverage" value="true" /> + <output name="output_html" ftype="html"> + <assert_contents> + <has_text text="Qualimap report: BAM QC" /> + </assert_contents> + </output> + <output name="output_per_base_coverage" file="per_base_coverage_default.txt" ftype="tsv" /> + <output_collection name="raw_data" type="list"> + <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" /> + </output_collection> + </test> + <test expect_num_outputs="12"> + <param name="input1" value="test_mapped_reads.bam"/> + <conditional name="stats_regions"> + <param name="region_select" value="custom_regions" /> + <param name="regions" value="features.gtf" /> + </conditional> + <output name="output_html" ftype="html"> + <assert_contents> + <has_text text="Qualimap report: BAM QC" /> + </assert_contents> + </output> + <output_collection name="raw_data" type="list"> + <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" /> + </output_collection> + </test> + <test expect_num_outputs="13"> + <param name="input1" value="test_mapped_reads.bam" /> + <conditional name="stats_regions"> + <param name="region_select" value="custom_regions" /> + <param name="regions" value="features.gtf" /> + </conditional> + <param name="per_base_coverage" value="true" /> + <output name="output_html" ftype="html"> + <assert_contents> + <has_text text="Qualimap report: BAM QC" /> + </assert_contents> + </output> + <output name="output_per_base_coverage" file="per_base_coverage_inside_features.txt" ftype="tsv" /> + <output_collection name="raw_data" type="list"> + <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" /> + </output_collection> + </test> + <test expect_num_outputs="13"> + <param name="input1" value="test_mapped_reads.bam" /> + <conditional name="stats_regions"> + <param name="region_select" value="custom_regions" /> + <param name="regions" value="features.gtf" /> + <param name="outside_stats" value="true" /> + </conditional> + <param name="per_base_coverage" value="true" /> + <output name="output_html" ftype="html"> + <assert_contents> + <has_text text="Qualimap report: BAM QC" /> + </assert_contents> + </output> + <output name="output_per_base_coverage" file="per_base_coverage_outside_features.txt" ftype="tsv" /> + <output_collection name="raw_data" type="list"> + <element name="genome_results" file="genome_results_outside_features.txt" ftype="txt" compare="diff" lines_diff="2" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ +**What it does** + +**Qualimap BAM QC** lets you evaluate the quality of aligned reads data in BAM +format. The tool summarizes basic statistics of the alignment (number of reads, +coverage, GC-content, etc.) and produces a number of useful graphs for their +interpretation. + +The analysis can be performed with any kind of sequencing data, such as +whole-genome sequencing, exome sequencing, RNA-seq or ChIP-seq data. + +In addition, it is possible to provide an annotation file so the results are +computed for the reads mapping inside (and optionally outside) of the +corresponding genomic regions, which can be especially useful for evaluating +target-enrichment sequencing studies. + +Input +===== + +*Mapped reads input dataset* + +The dataset holding the mapped reads to carry out the analysis with. + +*Dataset specifying regions* + +If you decide to calculate mapping statistics for selected regions of the +reference genome (instead of for the whole genome), you need to specify the +regions through this additional dataset in gtf, gff or bed format. + +.. class:: infomark + + A typical problem when working with regions (and genome annotation data, in general) is potential inconsistency between the chromosome names used in the mapped reads input versus those used to define the regions. In the case of the human genome, for example, UCSC data has chromosomes starting with a 'chr' prefix, which is lacking from Ensemble data. This simple form of the problem is handled by Qualimap: if chromosome names in the regions input have a 'chr' prefix, Qualimap will add that prefix to the mapped reads chromosome names as needed. For more complex cases you will have to adjust your inputs manually. + + +Parameters +---------- + +*Reference genome regions to calculate mapping statistics for* + +Choose whether you would like to have mapping statistics reported across + +- the entire reference genome + (as specified in the header of the mapped reads input) + +- specific regions of the reference + +In the second case, you need to select a *Dataset specifying regions* (see +above). Using the *Invert regions* switch you can then indicate whether you +want to select or exclude the regions in this dataset. + +*Generate per-base coverage output* + +*Skip duplicate reads* + +The tool lets you skip alignments of duplicate reads from the analysis. +Depending on whether you select none, either one, or both of the available +options, you can decide to: + +- not correct for duplicate reads at all (*e.g.* because you have removed them + at an earlier step with some dedicated tool) +- identify and flag duplicate reads with a dedicated tool (like ``Picard + MarkDuplicates`` or ``samtools markdup``), then have Qualimap ignore the + duplicate-flagged reads (recommended, most flexible option since other tools + can be told to ignore the same reads) +- have Qualimap identify potential duplicates by itself and ignore them +- combine external and Qualimap-internal duplicate detection for extra + stringency + +Independent of your selection, the HTML report will always list (in the +`Globals` section of the `Summary`) the number of duplicated reads estimated by +Qualimap. If you choose to skip duplicates, you will also be informed about the +number of skipped reads in that same section and, if you instruct Qualimap to +look for the duplicate flag on reads, the number of reads flagged as duplicates +will also be reported here. + +**Section: Settings affecting specific plots** + +Parameters in this section only affect some (or even only one) of the plots +contained in the HTML report (and the corresponding part of the *Raw Data* +output collection). + +For most of these options, the parameter help above should be descriptive +enough. Just a few more words on two of them: + +*Number of bins to use in across-reference plots* + +This value is used for computing the various graphs that plot information +across the reference. Basically, the reference genome gets split into the given +number of bins, and reads falling in the same bin are aggregated in the +statistics of that bin. + +Thus, the higher the number of bins, the higher the resolution of the plots, +but more bins also require longer time for their statistics to be computed. +Less bins, on the other hand, mean more reads will have to be aggregated per +bin and this comes with higher memory requirements. Hence, if the tool fails +with an ``Out Of Memory`` error, you may want to rerun it with a higher bin +number. + +*Plot expected GC-content distribution of the following reference genome* + +The choice of reference genomes with pre-calculated GC distributions is built +into Qualimap. + +Future releases of Qualimap may include more choices, but the current version +is limited to those offered here. + + +Outputs +======= + +HTML Report +----------- + +**Summary Section** + +*Globals* + +This section contains information about the total number of reads, number of mapped reads, paired-end mapping performance, read length distribution, +number of clipped reads and duplication rate (estimated from the start positions of read alignments). + +*ACGT Content* + +Nucleotide content and GC percentage in the mapped reads. + +*Coverage* + +Mean and standard deviation of the coverage depth. + +*Mapping quality* + +Mean mapping quality of the mapped reads. + +*Insert size* + +Mean, standard deviation and percentiles of the insert size distribution if applicable. The features are computed based on the TLEN field of the SAM file. + +*Mismatches and indels* + +The section reports general alignment error rate (computed as a ratio of total collected edit distance to the number of mapped bases), total number of mismatches and total number of indels (computed from the CIGAR values). Additionally fraction of the homopolymer indels among total indels is provided. Note, the error rate and mismatches metrics are based on optional fields of a SAM record (NM for edit distance, MD for mismatches). The features are not reported if these fields are missing in the SAM file. + +*Chromosome stats* + +Number of mapped bases, mean and standard deviation of the coverage depth for each chromosome as defined by the header of the SAM file. + +For region-based analysis the information is given inside of regions, including some additional information like, for example, number of correct strand reads. + + +**Plots** + +*Coverage Across Reference* + +This plot consists of two figures. +The upper figure provides the coverage distribution (red line) and coverage +deviation across the reference sequence. +The lower figure shows GC content across reference (black line) together with +its average value (red dotted line). + +*Coverage Histogram* + +Histogram of the number of genomic locations having a given coverage rate. +The bins of the x-axis are conveniently scaled by aggregating some coverage +values in order to produce a representative histogram also in presence of the +usual NGS peaks of coverage. + +*Coverage Histogram (0-50X)* + +Similar to the previous plot, but in this graph genome locations with a +coverage greater than 50X are grouped into the last bin. +By doing so a higher resolution of the most common values for the coverage rate +is obtained. + +*Genome Fraction Coverage* + +Provides a visual way of knowing how much reference has been sequenced to at +least a given coverage rate. +This graph should be interpreted as in this example: +If one aims for a coverage rate of at least 25X (x-axis), how much of the +reference (y-axis) will be considered? + +*Duplication Rate Histogram* + +This plot shows the distribution of duplicated reads. +Due to several factors (*e.g.* amount of starting material, sample preparation, +*etc.*) it is possible that the same fragments are sequenced several times. +For some experiments where enrichment is used (*e.g.* ChIP-seq ) this is +expected to some degree. +For most experiments, however, a high duplication level of the reads indicates +some unwanted bias. + +*Mapped Reads Nucleotide Content* + +This plot shows the nucleotide content per position of the mapped reads. + +*Mapped Reads GC Content Distribution* + +This graph shows the distribution of GC-content per mapped read. +If compared with a precomputed genome distribution, this plot allows to check +if there is a shift in the GC content. + +*Mapped Reads Clipping Profile* + +Represents the percentage of clipped bases across the reads. +Technically, the clipping is detected via SAM format CIGAR codes ‘H’ +(hard clipping) and ‘S’ (soft clipping). +In addition, the total number of clipped reads can be found in the report +`Summary` section. + +This plot is not shown if no clipped reads are found. + +*Homopolymer Indels* + +This bar plot shows the number of indels that are located within A, C, G and T +homopolymers, respectively, as well as the number of indels that are not within +any homopolymer. Large numbers of homopolymer indels may indicate a problem in +the sequencing process. +Technically, Qualimap identifies indels from the CIGAR code of the aligned +reads. Indel statistics can also be found in a dedicated section of the report +`Summary`. + +This graph is not shown if the sample doesn’t contain any indels. + +*Mapping Quality Across Reference* + +This plot provides the mapping quality distribution across the reference. +To construct the plot, the mean mapping quality is computed for each bin. + +*Mapping Quality Histogram* + +Histogram of the number of genomic locations having a given mapping quality. +To construct the histogram the mean mapping quality is computed at each genome +position with non-zero coverage and collected. +According to the SAM/BAM format specifications, the range for the mapping +quality score is [0-255]. + +*Insert Size Across Reference* + +This plot provides the insert size distribution across the reference. +Technically, the insert size of each pair of aligned reads is collected from +the SAM alignment field `TLEN`. Only positive values are taken into account. +To construct the plot, the mean insert size is computed for each bin. + +*Insert Size Histogram* + +Histogram of insert size distribution. + + +Raw Data +-------- + +This is a *Collection* of 10 individual datasets. + +The *genome_results* dataset provides a plain-text summary of key statistics, +most of which can also be found in the *Summary* section of the *HTML Report*. + +The remaining 9 datasets hold the tabular raw data underlying the plots of the corresponding names in the *HTML Report*. + + +Per-base coverage +----------------- + +Optional. This is a tabular dataset listing the coverage of every base in the +reference genome unless that coverage is zero. Since its content is +uncompressed text, this dataset can easily become huge, and it is recommended +that you generate this dataset only for very small genomes or very limited +regions of larger genomes. + ]]> </help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_macros.xml Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,40 @@ +<macros> + <token name="@VERSION@">2.2.2c</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">qualimap</requirement> + <yield /> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btv566</citation> + <citation type="doi">10.1093/bioinformatics/bts503</citation> + <yield /> + </citations> + </xml> + + <token name="@SET_JAVA_OPTS@"> + export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m" + </token> + + <token name="@MASSAGE_OUTPUT@"><![CDATA[ + sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' && + mkdir '${output_html.extra_files_path}' && + mv results/css/*.css '${output_html.extra_files_path}' && + mv results/css/*.png '${output_html.extra_files_path}' && + if [ -d results/images_${report_name} ]; then + mv results/images_${report_name}/* '${output_html.extra_files_path}' && + for file in \$(ls -A results/raw_data_${report_name}); do mv "results/raw_data_${report_name}/\$file" `echo "results/\$file" | sed 's/(//;s/)//'`; done + fi + #if $summary_report: + && mv results/$summary_report results/summary_report.txt + #end if + ]]></token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_across_reference.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,326 @@ +#Position (bp) Coverage Std +1.5 0.0 0.0 +3.5 0.0 0.0 +5.5 0.0 0.0 +7.5 0.0 0.0 +9.5 0.0 0.0 +11.5 0.0 0.0 +13.5 0.0 0.0 +15.5 0.0 0.0 +17.5 0.0 0.0 +19.5 0.0 0.0 +21.5 0.0 0.0 +23.5 0.0 0.0 +25.5 0.0 0.0 +27.5 0.0 0.0 +29.5 0.0 0.0 +31.5 0.0 0.0 +33.5 0.0 0.0 +35.5 0.0 0.0 +37.5 0.0 0.0 +39.5 0.0 0.0 +41.5 0.0 0.0 +43.5 0.0 0.0 +45.5 0.0 0.0 +47.5 0.0 0.0 +49.5 0.0 0.0 +51.5 0.0 0.0 +53.5 1.0 0.0 +55.5 2.5 1.5811388300841898 +57.5 3.5 1.8708286933869707 +59.5 4.0 0.0 +61.5 5.0 0.0 +63.5 5.0 0.0 +65.5 5.0 0.0 +67.5 5.0 0.0 +69.5 5.0 0.0 +71.5 5.5 2.345207879911715 +73.5 6.0 0.0 +75.5 6.0 0.0 +77.5 7.0 1.0 +79.5 8.0 0.0 +81.5 8.0 0.0 +83.5 9.0 0.0 +85.5 9.5 3.082207001484488 +87.5 10.5 3.24037034920393 +89.5 12.0 0.0 +91.5 13.5 3.6742346141747673 +93.5 15.0 1.0 +95.5 16.5 4.06201920231798 +97.5 17.5 4.183300132670378 +99.5 18.0 0.0 +101.5 21.5 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0.0 +569.5 0.0 0.0 +571.5 0.0 0.0 +573.5 0.0 0.0 +575.5 0.0 0.0 +577.5 0.0 0.0 +579.5 0.0 0.0 +581.5 0.0 0.0 +583.5 0.0 0.0 +585.5 0.0 0.0 +587.5 0.0 0.0 +589.5 0.0 0.0 +591.5 0.0 0.0 +593.5 0.0 0.0 +595.5 0.0 0.0 +597.5 0.0 0.0 +599.5 0.0 0.0 +601.5 0.0 0.0 +603.5 0.0 0.0 +605.5 0.0 0.0 +607.5 0.0 0.0 +609.5 0.0 0.0 +611.5 0.0 0.0 +613.5 0.0 0.0 +615.5 0.0 0.0 +617.5 0.0 0.0 +619.5 0.0 0.0 +621.5 0.0 0.0 +623.5 0.0 0.0 +625.5 0.0 0.0 +627.5 0.0 0.0 +629.5 0.0 0.0 +631.5 0.0 0.0 +633.5 0.0 0.0 +635.5 0.0 0.0 +637.5 0.0 0.0 +639.5 0.0 0.0 +641.5 0.0 0.0 +643.5 0.0 0.0 +645.5 0.0 0.0 +647.5 0.0 0.0 +649.5 0.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_histogram.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,36 @@ +#Coverage Number of genomic locations +0.0 102.0 +1.0 2.0 +2.0 1.0 +3.0 2.0 +4.0 3.0 +5.0 11.0 +6.0 6.0 +8.0 5.0 +9.0 3.0 +10.0 2.0 +11.0 1.0 +12.0 2.0 +13.0 1.0 +14.0 2.0 +16.0 2.0 +17.0 2.0 +18.0 3.0 +21.0 1.0 +22.0 1.0 +23.0 3.0 +24.0 1.0 +25.0 8.0 +26.0 7.0 +27.0 3.0 +28.0 8.0 +29.0 11.0 +30.0 10.0 +31.0 20.0 +32.0 27.0 +33.0 11.0 +34.0 5.0 +35.0 4.0 +36.0 13.0 +37.0 8.0 +38.0 9.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/duplication_rate_histogram.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,51 @@ +#Duplication rate Coverage +1.0 57.0 +2.0 8.0 +3.0 3.0 +4.0 0.0 +5.0 0.0 +6.0 0.0 +7.0 0.0 +8.0 0.0 +9.0 0.0 +10.0 0.0 +11.0 0.0 +12.0 0.0 +13.0 0.0 +14.0 0.0 +15.0 0.0 +16.0 0.0 +17.0 0.0 +18.0 0.0 +19.0 0.0 +20.0 0.0 +21.0 0.0 +22.0 0.0 +23.0 0.0 +24.0 0.0 +25.0 0.0 +26.0 0.0 +27.0 0.0 +28.0 0.0 +29.0 0.0 +30.0 0.0 +31.0 0.0 +32.0 0.0 +33.0 0.0 +34.0 0.0 +35.0 0.0 +36.0 0.0 +37.0 0.0 +38.0 0.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features.gtf Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,4 @@ +test_chromosome test gene 1 300 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test transcript 1 300 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test exon 1 300 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; +test_chromosome test CDS 100 250 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_fraction_coverage.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,52 @@ +#Coverage (X) Coverage +1.0 66.0 +2.0 65.33333333333334 +3.0 65.0 +4.0 64.33333333333334 +5.0 63.333333333333336 +6.0 59.66666666666667 +7.0 57.66666666666667 +8.0 57.66666666666667 +9.0 56.00000000000001 +10.0 55.00000000000001 +11.0 54.33333333333334 +12.0 54.00000000000001 +13.0 53.33333333333334 +14.0 53.00000000000001 +15.0 52.33333333333334 +16.0 52.33333333333334 +17.0 51.66666666666668 +18.0 51.000000000000014 +19.0 50.000000000000014 +20.0 50.000000000000014 +21.0 50.000000000000014 +22.0 49.66666666666668 +23.0 49.33333333333334 +24.0 48.33333333333334 +25.0 48.00000000000001 +26.0 45.33333333333334 +27.0 43.00000000000001 +28.0 42.00000000000001 +29.0 39.33333333333334 +30.0 35.66666666666667 +31.0 32.33333333333334 +32.0 25.66666666666667 +33.0 16.66666666666667 +34.0 13.0 +35.0 11.333333333333329 +36.0 10.0 +37.0 5.666666666666671 +38.0 3.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0 +51.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_default.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,122 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmprT4oZK/files/b/1/f/dataset_b1fbaad4-1b5a-4769-8a15-b4cec4de5731.dat + outfile = results/genome_results.txt + + +>>>>>>> Reference + + number of bases = 650 bp + number of contigs = 1 + + +>>>>>>> Globals + + number of windows = 325 + + number of reads = 100 + number of mapped reads = 100 (100%) + number of secondary alignments = 1 + + number of mapped bases = 12,665 bp + number of sequenced bases = 7,465 bp + number of aligned bases = 0 bp + number of duplicated reads (estimated) = 18 + duplication rate = 15.85% + + +>>>>>>> Insert size + + mean insert size = 0 + std insert size = 0 + median insert size = 0 + + +>>>>>>> Mapping quality + + mean mapping quality = 115.8402 + + +>>>>>>> ACTG content + + number of A's = 1,910 bp (25.59%) + number of C's = 1,902 bp (25.48%) + number of T's = 1,497 bp (20.05%) + number of G's = 2,156 bp (28.88%) + number of N's = 0 bp (0%) + + GC percentage = 54.36% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0118 + number of mismatches = 149 + + +>>>>>>> Coverage + + mean coverageData = 19.4846X + std coverageData = 16.5813X + + There is a 45.85% of reference with a coverageData >= 1X + There is a 45.38% of reference with a coverageData >= 2X + There is a 44.92% of reference with a coverageData >= 3X + There is a 44.62% of reference with a coverageData >= 4X + There is a 43.85% of reference with a coverageData >= 5X + There is a 41.85% of reference with a coverageData >= 6X + There is a 40.46% of reference with a coverageData >= 7X + There is a 39.85% of reference with a coverageData >= 8X + There is a 38.77% of reference with a coverageData >= 9X + There is a 38% of reference with a coverageData >= 10X + There is a 37.23% of reference with a coverageData >= 11X + There is a 36.92% of reference with a coverageData >= 12X + There is a 36.46% of reference with a coverageData >= 13X + There is a 36.15% of reference with a coverageData >= 14X + There is a 35.54% of reference with a coverageData >= 15X + There is a 35.23% of reference with a coverageData >= 16X + There is a 34.77% of reference with a coverageData >= 17X + There is a 34% of reference with a coverageData >= 18X + There is a 33.38% of reference with a coverageData >= 19X + There is a 33.38% of reference with a coverageData >= 20X + There is a 33.23% of reference with a coverageData >= 21X + There is a 31.85% of reference with a coverageData >= 22X + There is a 31.54% of reference with a coverageData >= 23X + There is a 30.92% of reference with a coverageData >= 24X + There is a 30.62% of reference with a coverageData >= 25X + There is a 28.62% of reference with a coverageData >= 26X + There is a 27.54% of reference with a coverageData >= 27X + There is a 26.92% of reference with a coverageData >= 28X + There is a 25.23% of reference with a coverageData >= 29X + There is a 23.38% of reference with a coverageData >= 30X + There is a 20.77% of reference with a coverageData >= 31X + There is a 16.77% of reference with a coverageData >= 32X + There is a 12.15% of reference with a coverageData >= 33X + There is a 10.15% of reference with a coverageData >= 34X + There is a 8.62% of reference with a coverageData >= 35X + There is a 7.38% of reference with a coverageData >= 36X + There is a 4% of reference with a coverageData >= 37X + There is a 1.85% of reference with a coverageData >= 38X + There is a 0.31% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + test_chromosome 650 12665 19.484615384615385 16.581284452141826 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_inside_features.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,128 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmpB4Sf0A/files/e/d/7/dataset_ed7510d4-c8f3-41fc-8cc1-3b854d9bdf14.dat + outfile = results/genome_results.txt + + +>>>>>>> Reference + + number of bases = 650 bp + number of contigs = 1 + + +>>>>>>> Globals + + number of windows = 325 + + number of reads = 100 + number of mapped reads = 100 (100%) + number of secondary alignments = 1 + + number of mapped bases = 6,451 bp + number of sequenced bases = 5,101 bp + number of aligned bases = 0 bp + number of duplicated reads (estimated) = 14 + duplication rate = 16.18% + + +>>>>>>> Globals inside + + regions size = 300 (46.15%) + number of mapped reads = 82 (82%) + + +>>>>>>> Insert size + + mean insert size = 0 + std insert size = 0 + median insert size = 0 + + +>>>>>>> Mapping quality + + mean mapping quality = 251.3687 + + +>>>>>>> ACTG content + + number of A's = 1,243 bp (24.37%) + number of C's = 1,257 bp (24.64%) + number of T's = 985 bp (19.31%) + number of G's = 1,616 bp (31.68%) + number of N's = 0 bp (0%) + + GC percentage = 56.32% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0211 + number of mismatches = 136 + + +>>>>>>> Coverage + + mean coverageData = 21.5033X + std coverageData = 15.658X + + There is a 66% of reference with a coverageData >= 1X + There is a 65.33% of reference with a coverageData >= 2X + There is a 65% of reference with a coverageData >= 3X + There is a 64.33% of reference with a coverageData >= 4X + There is a 63.33% of reference with a coverageData >= 5X + There is a 59.67% of reference with a coverageData >= 6X + There is a 57.67% of reference with a coverageData >= 7X + There is a 57.67% of reference with a coverageData >= 8X + There is a 56% of reference with a coverageData >= 9X + There is a 55% of reference with a coverageData >= 10X + There is a 54.33% of reference with a coverageData >= 11X + There is a 54% of reference with a coverageData >= 12X + There is a 53.33% of reference with a coverageData >= 13X + There is a 53% of reference with a coverageData >= 14X + There is a 52.33% of reference with a coverageData >= 15X + There is a 52.33% of reference with a coverageData >= 16X + There is a 51.67% of reference with a coverageData >= 17X + There is a 51% of reference with a coverageData >= 18X + There is a 50% of reference with a coverageData >= 19X + There is a 50% of reference with a coverageData >= 20X + There is a 50% of reference with a coverageData >= 21X + There is a 49.67% of reference with a coverageData >= 22X + There is a 49.33% of reference with a coverageData >= 23X + There is a 48.33% of reference with a coverageData >= 24X + There is a 48% of reference with a coverageData >= 25X + There is a 45.33% of reference with a coverageData >= 26X + There is a 43% of reference with a coverageData >= 27X + There is a 42% of reference with a coverageData >= 28X + There is a 39.33% of reference with a coverageData >= 29X + There is a 35.67% of reference with a coverageData >= 30X + There is a 32.33% of reference with a coverageData >= 31X + There is a 25.67% of reference with a coverageData >= 32X + There is a 16.67% of reference with a coverageData >= 33X + There is a 13% of reference with a coverageData >= 34X + There is a 11.33% of reference with a coverageData >= 35X + There is a 10% of reference with a coverageData >= 36X + There is a 5.67% of reference with a coverageData >= 37X + There is a 3% of reference with a coverageData >= 38X + There is a 0% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + test_chromosome 300 6451 21.503333333333334 15.658011438947867 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_outside_features.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,128 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmprT4oZK/files/6/4/1/dataset_6416c0ca-3ecd-4273-ae01-22f2ac60965d.dat + outfile = results/outside_results.txt + + +>>>>>>> Reference + + number of bases = 650 bp + number of contigs = 1 + + +>>>>>>> Globals + + number of windows = 325 + + number of reads = 100 + number of mapped reads = 100 (100%) + number of secondary alignments = 1 + + number of mapped bases = 6,214 bp + number of sequenced bases = 2,364 bp + number of aligned bases = 0 bp + number of duplicated reads (estimated) = 4 + duplication rate = 14.29% + + +>>>>>>> Globals outside + + regions size = 350 (53.85%) + number of mapped reads = 18 (18%) + + +>>>>>>> Insert size + + mean insert size = 0 + std insert size = 0 + median insert size = 0 + + +>>>>>>> Mapping quality + + mean mapping quality = 255 + + +>>>>>>> ACTG content + + number of A's = 667 bp (28.21%) + number of C's = 645 bp (27.28%) + number of T's = 512 bp (21.66%) + number of G's = 540 bp (22.84%) + number of N's = 0 bp (0%) + + GC percentage = 50.13% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0021 + number of mismatches = 13 + + +>>>>>>> Coverage + + mean coverageData = 17.7543X + std coverageData = 16.4764X + + There is a 10.58% of reference with a coverageData >= 1X + There is a 10.58% of reference with a coverageData >= 2X + There is a 10.58% of reference with a coverageData >= 3X + There is a 10.58% of reference with a coverageData >= 4X + There is a 10.58% of reference with a coverageData >= 5X + There is a 10.58% of reference with a coverageData >= 6X + There is a 10.58% of reference with a coverageData >= 7X + There is a 10.58% of reference with a coverageData >= 8X + There is a 10.58% of reference with a coverageData >= 9X + There is a 10.58% of reference with a coverageData >= 10X + There is a 10.58% of reference with a coverageData >= 11X + There is a 10.58% of reference with a coverageData >= 12X + There is a 10.58% of reference with a coverageData >= 13X + There is a 10.58% of reference with a coverageData >= 14X + There is a 10.58% of reference with a coverageData >= 15X + There is a 10.58% of reference with a coverageData >= 16X + There is a 10.58% of reference with a coverageData >= 17X + There is a 10.58% of reference with a coverageData >= 18X + There is a 10.58% of reference with a coverageData >= 19X + There is a 10.58% of reference with a coverageData >= 20X + There is a 10.58% of reference with a coverageData >= 21X + There is a 10.58% of reference with a coverageData >= 22X + There is a 10.58% of reference with a coverageData >= 23X + There is a 10.58% of reference with a coverageData >= 24X + There is a 10.58% of reference with a coverageData >= 25X + There is a 10.58% of reference with a coverageData >= 26X + There is a 10.58% of reference with a coverageData >= 27X + There is a 10.58% of reference with a coverageData >= 28X + There is a 10.58% of reference with a coverageData >= 29X + There is a 10.58% of reference with a coverageData >= 30X + There is a 10.58% of reference with a coverageData >= 31X + There is a 10.1% of reference with a coverageData >= 32X + There is a 9.62% of reference with a coverageData >= 33X + There is a 9.13% of reference with a coverageData >= 34X + There is a 7.21% of reference with a coverageData >= 35X + There is a 5.29% of reference with a coverageData >= 36X + There is a 3.37% of reference with a coverageData >= 37X + There is a 1.44% of reference with a coverageData >= 38X + There is a 0.96% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + test_chromosome 4424 6214 1.404611211573237 3.9981701358234454 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_clipping_profile.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,76 @@ +#Read position (bp) Clipping profile +0.0 16.666666666666664 +1.0 5.555555555555555 +2.0 0.0 +3.0 0.0 +4.0 0.0 +5.0 0.0 +6.0 0.0 +7.0 0.0 +8.0 0.0 +9.0 0.0 +10.0 0.0 +11.0 0.0 +12.0 0.0 +13.0 0.0 +14.0 0.0 +15.0 0.0 +16.0 0.0 +17.0 0.0 +18.0 0.0 +19.0 0.0 +20.0 0.0 +21.0 0.0 +22.0 0.0 +23.0 0.0 +24.0 0.0 +25.0 0.0 +26.0 0.0 +27.0 0.0 +28.0 0.0 +29.0 0.0 +30.0 0.0 +31.0 0.0 +32.0 0.0 +33.0 0.0 +34.0 0.0 +35.0 0.0 +36.0 0.0 +37.0 0.0 +38.0 0.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0 +51.0 0.0 +52.0 0.0 +53.0 0.0 +54.0 0.0 +55.0 0.0 +56.0 0.0 +57.0 0.0 +58.0 0.0 +59.0 0.0 +60.0 0.0 +61.0 0.0 +62.0 0.0 +63.0 0.0 +64.0 0.0 +65.0 0.0 +66.0 0.0 +67.0 0.0 +68.0 0.0 +69.0 0.0 +70.0 0.0 +71.0 5.555555555555555 +72.0 11.11111111111111 +73.0 16.666666666666664 +74.0 44.44444444444444
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_gc-content_distribution.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,101 @@ +#GC Content (%) Sample HUMAN (hg19) +1.0 0.0 0.0 +2.0 0.0 3.0E-6 +3.0 0.0 3.0E-6 +4.0 0.0 1.0E-5 +5.0 0.0 8.0E-6 +6.0 0.0 1.2000000000000002E-5 +7.0 0.0 6.999999999999999E-6 +8.0 0.0 9.999999999999999E-6 +9.0 0.0 1.6E-5 +10.0 0.0 1.5000000000000002E-5 +11.0 0.0 1.9999999999999998E-5 +12.0 0.0 1.6E-5 +13.0 0.0 1.6E-5 +14.0 0.0 2.4999999999999998E-5 +15.0 0.0 2.2000000000000003E-5 +16.0 0.0 2.6999999999999996E-5 +17.0 0.0 3.3E-5 +18.0 0.0 3.7000000000000005E-5 +19.0 0.0 4.7000000000000004E-5 +20.0 0.0 5.4999999999999995E-5 +21.0 0.0 6.400000000000001E-5 +22.0 0.0 9.3E-5 +23.0 0.0 1.66E-4 +24.0 0.0 3.03E-4 +25.0 0.0 7.059999999999999E-4 +26.0 0.0 0.0016020000000000001 +27.0 0.0 0.0033690000000000005 +28.0 0.0 0.006167999999999999 +29.0 0.0 0.010352 +30.0 0.0 0.015647 +31.0 0.0 0.022148 +32.0 0.0 0.028808 +33.0 0.0 0.035106000000000005 +34.0 0.0 0.041161 +35.0 0.0 0.047408 +36.0 0.0 0.052698999999999996 +37.0 0.0 0.057517000000000006 +38.0 0.0 0.061487999999999994 +39.0 0.0 0.063321 +40.0 0.0 0.060248 +41.0 0.0 0.055508 +42.0 0.0 0.051446000000000006 +43.0 0.0 0.048194 +44.0 0.017857142857142856 0.044423 +45.0 0.0 0.040655000000000004 +46.0 0.03571428571428571 0.03652 +47.0 0.0 0.032315 +48.0 0.017857142857142856 0.028137999999999996 +49.0 0.0 0.02458 +50.0 0.017857142857142856 0.020810000000000002 +51.0 0.0 0.017532 +52.0 0.05357142857142857 0.014506999999999997 +53.0 0.017857142857142856 0.012007 +54.0 0.14285714285714285 0.010018 +55.0 0.08928571428571429 0.008414999999999999 +56.0 0.17857142857142855 0.007258 +57.0 0.03571428571428571 0.006174999999999999 +58.0 0.08928571428571429 0.005363000000000001 +59.0 0.03571428571428571 0.0046159999999999994 +60.0 0.14285714285714285 0.003946 +61.0 0.0 0.0034579999999999993 +62.0 0.03571428571428571 0.002915 +63.0 0.017857142857142856 0.0024610000000000005 +64.0 0.05357142857142857 0.0019950000000000002 +65.0 0.0 0.0016779999999999998 +66.0 0.017857142857142856 0.0013500000000000003 +67.0 0.0 0.001069 +68.0 0.0 8.119999999999999E-4 +69.0 0.0 6.4E-4 +70.0 0.0 5.05E-4 +71.0 0.0 4.0299999999999993E-4 +72.0 0.0 3.2E-4 +73.0 0.0 2.79E-4 +74.0 0.0 2.0700000000000002E-4 +75.0 0.0 2.0099999999999998E-4 +76.0 0.0 1.54E-4 +77.0 0.0 1.12E-4 +78.0 0.0 7.699999999999999E-5 +79.0 0.0 6.3E-5 +80.0 0.0 3.7E-5 +81.0 0.0 2.8000000000000003E-5 +82.0 0.0 1.6E-5 +83.0 0.0 9.0E-6 +84.0 0.0 4.0E-6 +85.0 0.0 0.0 +86.0 0.0 1.0E-6 +87.0 0.0 0.0 +88.0 0.0 0.0 +89.0 0.0 0.0 +90.0 0.0 0.0 +91.0 0.0 0.0 +92.0 0.0 0.0 +93.0 0.0 0.0 +94.0 0.0 0.0 +95.0 0.0 0.0 +96.0 0.0 0.0 +97.0 0.0 0.0 +98.0 0.0 0.0 +99.0 0.0 0.0 +100.0 0.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_nucleotide_content.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,76 @@ +# Position (bp) A C G T N +0.0 34.177215189873415 21.518987341772153 26.582278481012654 17.72151898734177 0.0 +1.0 23.456790123456788 33.33333333333333 20.98765432098765 22.22222222222222 0.0 +2.0 25.609756097560975 20.73170731707317 35.36585365853659 18.29268292682927 0.0 +3.0 23.170731707317074 28.04878048780488 28.04878048780488 20.73170731707317 0.0 +4.0 31.70731707317073 26.82926829268293 24.390243902439025 17.073170731707318 0.0 +5.0 25.609756097560975 19.51219512195122 34.146341463414636 20.73170731707317 0.0 +6.0 25.609756097560975 23.170731707317074 34.146341463414636 17.073170731707318 0.0 +7.0 28.04878048780488 21.951219512195124 30.48780487804878 19.51219512195122 0.0 +8.0 23.170731707317074 18.29268292682927 39.02439024390244 19.51219512195122 0.0 +9.0 28.04878048780488 29.268292682926827 24.390243902439025 18.29268292682927 0.0 +10.0 24.390243902439025 23.170731707317074 34.146341463414636 18.29268292682927 0.0 +11.0 19.51219512195122 31.70731707317073 28.04878048780488 20.73170731707317 0.0 +12.0 34.146341463414636 23.170731707317074 28.04878048780488 14.634146341463413 0.0 +13.0 26.82926829268293 18.29268292682927 36.58536585365854 18.29268292682927 0.0 +14.0 24.390243902439025 26.82926829268293 29.268292682926827 19.51219512195122 0.0 +15.0 29.268292682926827 21.951219512195124 28.04878048780488 20.73170731707317 0.0 +16.0 31.70731707317073 25.609756097560975 29.268292682926827 13.414634146341465 0.0 +17.0 15.853658536585366 25.609756097560975 35.36585365853659 23.170731707317074 0.0 +18.0 31.70731707317073 17.073170731707318 31.70731707317073 19.51219512195122 0.0 +19.0 24.390243902439025 29.268292682926827 29.268292682926827 17.073170731707318 0.0 +20.0 21.951219512195124 25.609756097560975 29.268292682926827 23.170731707317074 0.0 +21.0 23.170731707317074 28.04878048780488 36.58536585365854 12.195121951219512 0.0 +22.0 28.04878048780488 30.48780487804878 18.29268292682927 23.170731707317074 0.0 +23.0 23.170731707317074 18.29268292682927 29.268292682926827 29.268292682926827 0.0 +24.0 25.609756097560975 19.51219512195122 35.36585365853659 19.51219512195122 0.0 +25.0 23.170731707317074 26.82926829268293 25.609756097560975 24.390243902439025 0.0 +26.0 21.951219512195124 19.51219512195122 41.46341463414634 17.073170731707318 0.0 +27.0 18.29268292682927 29.268292682926827 35.36585365853659 17.073170731707318 0.0 +28.0 29.268292682926827 30.48780487804878 25.609756097560975 14.634146341463413 0.0 +29.0 17.073170731707318 25.609756097560975 36.58536585365854 20.73170731707317 0.0 +30.0 25.609756097560975 21.951219512195124 32.926829268292686 19.51219512195122 0.0 +31.0 29.268292682926827 23.170731707317074 32.926829268292686 14.634146341463413 0.0 +32.0 29.268292682926827 21.951219512195124 24.390243902439025 24.390243902439025 0.0 +33.0 20.73170731707317 31.70731707317073 26.82926829268293 20.73170731707317 0.0 +34.0 18.29268292682927 20.73170731707317 40.243902439024396 20.73170731707317 0.0 +35.0 37.80487804878049 13.414634146341465 28.04878048780488 20.73170731707317 0.0 +36.0 28.04878048780488 28.04878048780488 28.04878048780488 15.853658536585366 0.0 +37.0 21.951219512195124 20.73170731707317 39.02439024390244 18.29268292682927 0.0 +38.0 34.146341463414636 26.82926829268293 14.634146341463413 24.390243902439025 0.0 +39.0 31.70731707317073 17.073170731707318 26.82926829268293 24.390243902439025 0.0 +40.0 26.82926829268293 24.390243902439025 31.70731707317073 17.073170731707318 0.0 +41.0 30.48780487804878 19.51219512195122 25.609756097560975 24.390243902439025 0.0 +42.0 15.853658536585366 25.609756097560975 34.146341463414636 24.390243902439025 0.0 +43.0 29.268292682926827 24.390243902439025 28.04878048780488 18.29268292682927 0.0 +44.0 26.82926829268293 24.390243902439025 31.70731707317073 17.073170731707318 0.0 +45.0 29.268292682926827 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_quality_across_reference.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,326 @@ +#Position (bp) mapping quality +1.5 0.0 +3.5 0.0 +5.5 0.0 +7.5 0.0 +9.5 0.0 +11.5 0.0 +13.5 0.0 +15.5 0.0 +17.5 0.0 +19.5 0.0 +21.5 0.0 +23.5 0.0 +25.5 0.0 +27.5 0.0 +29.5 0.0 +31.5 0.0 +33.5 0.0 +35.5 0.0 +37.5 0.0 +39.5 0.0 +41.5 0.0 +43.5 0.0 +45.5 0.0 +47.5 0.0 +49.5 0.0 +51.5 0.0 +53.5 255.0 +55.5 255.0 +57.5 255.0 +59.5 255.0 +61.5 255.0 +63.5 255.0 +65.5 255.0 +67.5 255.0 +69.5 255.0 +71.5 255.0 +73.5 255.0 +75.5 255.0 +77.5 255.0 +79.5 255.0 +81.5 255.0 +83.5 255.0 +85.5 255.0 +87.5 255.0 +89.5 255.0 +91.5 236.33333333333334 +93.5 238.2 +95.5 239.72727272727272 +97.5 240.6 +99.5 241.0 +101.5 243.27906976744185 +103.5 244.04347826086956 +105.5 244.27659574468086 +107.5 244.92 +109.5 244.92 +111.5 244.92 +113.5 244.92 +115.5 245.30769230769232 +117.5 245.30769230769232 +119.5 245.30769230769232 +121.5 245.49056603773585 +123.5 246.31034482758622 +125.5 247.125 +127.5 247.36363636363637 +129.5 247.24615384615385 +131.5 247.24615384615385 +133.5 247.125 +135.5 247.47761194029852 +137.5 247.36363636363637 +139.5 247.58823529411765 +141.5 248.0 +143.5 248.28 +145.5 248.3684210526316 +147.5 248.3684210526316 +149.5 248.3684210526316 +151.5 248.3684210526316 +153.5 248.0 +155.5 248.1891891891892 +157.5 248.0958904109589 +159.5 248.0958904109589 +161.5 248.0958904109589 +163.5 247.90140845070422 +165.5 251.54794520547946 +167.5 255.0 +169.5 255.0 +171.5 255.0 +173.5 255.0 +175.5 255.0 +177.5 255.0 +179.5 255.0 +181.5 255.0 +183.5 255.0 +185.5 255.0 +187.5 255.0 +189.5 255.0 +191.5 255.0 +193.5 255.0 +195.5 255.0 +197.5 255.0 +199.5 255.0 +201.5 255.0 +203.5 255.0 +205.5 255.0 +207.5 255.0 +209.5 255.0 +211.5 255.0 +213.5 255.0 +215.5 255.0 +217.5 255.0 +219.5 255.0 +221.5 255.0 +223.5 255.0 +225.5 255.0 +227.5 255.0 +229.5 255.0 +231.5 255.0 +233.5 255.0 +235.5 255.0 +237.5 255.0 +239.5 255.0 +241.5 255.0 +243.5 255.0 +245.5 255.0 +247.5 255.0 +249.5 255.0 +251.5 0.0 +253.5 0.0 +255.5 0.0 +257.5 0.0 +259.5 0.0 +261.5 0.0 +263.5 0.0 +265.5 0.0 +267.5 0.0 +269.5 0.0 +271.5 0.0 +273.5 0.0 +275.5 0.0 +277.5 0.0 +279.5 0.0 +281.5 0.0 +283.5 0.0 +285.5 0.0 +287.5 0.0 +289.5 0.0 +291.5 0.0 +293.5 0.0 +295.5 0.0 +297.5 0.0 +299.5 0.0 +301.5 0.0 +303.5 0.0 +305.5 0.0 +307.5 0.0 +309.5 0.0 +311.5 0.0 +313.5 0.0 +315.5 0.0 +317.5 0.0 +319.5 0.0 +321.5 0.0 +323.5 0.0 +325.5 0.0 +327.5 0.0 +329.5 0.0 +331.5 0.0 +333.5 0.0 +335.5 0.0 +337.5 0.0 +339.5 0.0 +341.5 0.0 +343.5 0.0 +345.5 0.0 +347.5 0.0 +349.5 0.0 +351.5 0.0 +353.5 0.0 +355.5 0.0 +357.5 0.0 +359.5 0.0 +361.5 0.0 +363.5 0.0 +365.5 0.0 +367.5 0.0 +369.5 0.0 +371.5 0.0 +373.5 0.0 +375.5 0.0 +377.5 0.0 +379.5 0.0 +381.5 0.0 +383.5 0.0 +385.5 0.0 +387.5 0.0 +389.5 0.0 +391.5 0.0 +393.5 0.0 +395.5 0.0 +397.5 0.0 +399.5 0.0 +401.5 0.0 +403.5 0.0 +405.5 0.0 +407.5 0.0 +409.5 0.0 +411.5 0.0 +413.5 0.0 +415.5 0.0 +417.5 0.0 +419.5 0.0 +421.5 0.0 +423.5 0.0 +425.5 0.0 +427.5 0.0 +429.5 0.0 +431.5 0.0 +433.5 0.0 +435.5 0.0 +437.5 0.0 +439.5 0.0 +441.5 0.0 +443.5 0.0 +445.5 0.0 +447.5 0.0 +449.5 0.0 +451.5 0.0 +453.5 0.0 +455.5 0.0 +457.5 0.0 +459.5 0.0 +461.5 0.0 +463.5 0.0 +465.5 0.0 +467.5 0.0 +469.5 0.0 +471.5 0.0 +473.5 0.0 +475.5 0.0 +477.5 0.0 +479.5 0.0 +481.5 0.0 +483.5 0.0 +485.5 0.0 +487.5 0.0 +489.5 0.0 +491.5 0.0 +493.5 0.0 +495.5 0.0 +497.5 0.0 +499.5 0.0 +501.5 0.0 +503.5 0.0 +505.5 0.0 +507.5 0.0 +509.5 0.0 +511.5 0.0 +513.5 0.0 +515.5 0.0 +517.5 0.0 +519.5 0.0 +521.5 0.0 +523.5 0.0 +525.5 0.0 +527.5 0.0 +529.5 0.0 +531.5 0.0 +533.5 0.0 +535.5 0.0 +537.5 0.0 +539.5 0.0 +541.5 0.0 +543.5 0.0 +545.5 0.0 +547.5 0.0 +549.5 0.0 +551.5 0.0 +553.5 0.0 +555.5 0.0 +557.5 0.0 +559.5 0.0 +561.5 0.0 +563.5 0.0 +565.5 0.0 +567.5 0.0 +569.5 0.0 +571.5 0.0 +573.5 0.0 +575.5 0.0 +577.5 0.0 +579.5 0.0 +581.5 0.0 +583.5 0.0 +585.5 0.0 +587.5 0.0 +589.5 0.0 +591.5 0.0 +593.5 0.0 +595.5 0.0 +597.5 0.0 +599.5 0.0 +601.5 0.0 +603.5 0.0 +605.5 0.0 +607.5 0.0 +609.5 0.0 +611.5 0.0 +613.5 0.0 +615.5 0.0 +617.5 0.0 +619.5 0.0 +621.5 0.0 +623.5 0.0 +625.5 0.0 +627.5 0.0 +629.5 0.0 +631.5 0.0 +633.5 0.0 +635.5 0.0 +637.5 0.0 +639.5 0.0 +641.5 0.0 +643.5 0.0 +645.5 0.0 +647.5 0.0 +649.5 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_quality_histogram.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,13 @@ +#Mapping quality mapping quality +235.0 1.0 +237.0 2.0 +239.0 2.0 +240.0 2.0 +241.0 3.0 +243.0 2.0 +244.0 12.0 +245.0 8.0 +246.0 2.0 +247.0 18.0 +248.0 23.0 +255.0 123.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse_counts_ensemble_1000_6.tsv Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,1000 @@ +#gene -GlcN01 -GlcN02 -GlcN03 +GlcN01 +GlcN02 +GlcN03 +ENSMUSG00000085214 641 542 776 491 791 368 +ENSMUSG00000096956 73 17 47 32 29 63 +ENSMUSG00000021252 2359 1563 2497 2126 2149 1296 +ENSMUSG00000046840 39 165 124 83 144 31 +ENSMUSG00000044062 1 0 3 6 1 0 +ENSMUSG00000007777 292 184 220 228 237 270 +ENSMUSG00000037361 421 300 380 316 393 310 +ENSMUSG00000043644 16 5 7 6 6 8 +ENSMUSG00000024442 812 566 727 569 784 692 +ENSMUSG00000042208 445 273 375 305 410 399 +ENSMUSG00000020831 5 4 5 6 6 3 +ENSMUSG00000025731 1259 942 1113 888 1585 1076 +ENSMUSG00000096232 394 309 396 261 417 306 +ENSMUSG00000055312 53 53 59 43 63 35 +ENSMUSG00000058706 948 581 835 716 927 622 +ENSMUSG00000001418 1440 813 1052 1092 1044 1168 +ENSMUSG00000028608 305 208 262 229 273 225 +ENSMUSG00000089900 3 3 2 7 4 5 +ENSMUSG00000058812 51 30 45 41 32 35 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/per_base_coverage_inside_features.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,199 @@ +#chr pos coverage +test_chromosome 53 1 +test_chromosome 54 1 +test_chromosome 55 2 +test_chromosome 56 3 +test_chromosome 57 3 +test_chromosome 58 4 +test_chromosome 59 4 +test_chromosome 60 4 +test_chromosome 61 5 +test_chromosome 62 5 +test_chromosome 63 5 +test_chromosome 64 5 +test_chromosome 65 5 +test_chromosome 66 5 +test_chromosome 67 5 +test_chromosome 68 5 +test_chromosome 69 5 +test_chromosome 70 5 +test_chromosome 71 5 +test_chromosome 72 6 +test_chromosome 73 6 +test_chromosome 74 6 +test_chromosome 75 6 +test_chromosome 76 6 +test_chromosome 77 6 +test_chromosome 78 8 +test_chromosome 79 8 +test_chromosome 80 8 +test_chromosome 81 8 +test_chromosome 82 8 +test_chromosome 83 9 +test_chromosome 84 9 +test_chromosome 85 9 +test_chromosome 86 10 +test_chromosome 87 10 +test_chromosome 88 11 +test_chromosome 89 12 +test_chromosome 90 12 +test_chromosome 91 13 +test_chromosome 92 14 +test_chromosome 93 14 +test_chromosome 94 16 +test_chromosome 95 16 +test_chromosome 96 17 +test_chromosome 97 17 +test_chromosome 98 18 +test_chromosome 99 18 +test_chromosome 100 18 +test_chromosome 101 21 +test_chromosome 102 22 +test_chromosome 103 23 +test_chromosome 104 23 +test_chromosome 105 23 +test_chromosome 106 24 +test_chromosome 107 25 +test_chromosome 108 25 +test_chromosome 109 25 +test_chromosome 110 25 +test_chromosome 111 25 +test_chromosome 112 25 +test_chromosome 113 25 +test_chromosome 114 25 +test_chromosome 115 26 +test_chromosome 116 26 +test_chromosome 117 26 +test_chromosome 118 26 +test_chromosome 119 26 +test_chromosome 120 26 +test_chromosome 121 26 +test_chromosome 122 27 +test_chromosome 123 29 +test_chromosome 124 29 +test_chromosome 125 32 +test_chromosome 126 32 +test_chromosome 127 33 +test_chromosome 128 33 +test_chromosome 129 33 +test_chromosome 130 32 +test_chromosome 131 32 +test_chromosome 132 33 +test_chromosome 133 32 +test_chromosome 134 32 +test_chromosome 135 34 +test_chromosome 136 33 +test_chromosome 137 33 +test_chromosome 138 33 +test_chromosome 139 34 +test_chromosome 140 34 +test_chromosome 141 35 +test_chromosome 142 37 +test_chromosome 143 37 +test_chromosome 144 38 +test_chromosome 145 38 +test_chromosome 146 38 +test_chromosome 147 38 +test_chromosome 148 38 +test_chromosome 149 38 +test_chromosome 150 38 +test_chromosome 151 38 +test_chromosome 152 38 +test_chromosome 153 36 +test_chromosome 154 36 +test_chromosome 155 37 +test_chromosome 156 37 +test_chromosome 157 37 +test_chromosome 158 36 +test_chromosome 159 36 +test_chromosome 160 37 +test_chromosome 161 36 +test_chromosome 162 37 +test_chromosome 163 36 +test_chromosome 164 35 +test_chromosome 165 37 +test_chromosome 166 36 +test_chromosome 167 36 +test_chromosome 168 36 +test_chromosome 169 34 +test_chromosome 170 36 +test_chromosome 171 36 +test_chromosome 172 36 +test_chromosome 173 35 +test_chromosome 174 35 +test_chromosome 175 36 +test_chromosome 176 33 +test_chromosome 177 32 +test_chromosome 178 32 +test_chromosome 179 32 +test_chromosome 180 32 +test_chromosome 181 32 +test_chromosome 182 31 +test_chromosome 183 31 +test_chromosome 184 32 +test_chromosome 185 32 +test_chromosome 186 32 +test_chromosome 187 32 +test_chromosome 188 32 +test_chromosome 189 32 +test_chromosome 190 31 +test_chromosome 191 31 +test_chromosome 192 31 +test_chromosome 193 31 +test_chromosome 194 32 +test_chromosome 195 32 +test_chromosome 196 32 +test_chromosome 197 32 +test_chromosome 198 30 +test_chromosome 199 29 +test_chromosome 200 28 +test_chromosome 201 31 +test_chromosome 202 30 +test_chromosome 203 29 +test_chromosome 204 30 +test_chromosome 205 31 +test_chromosome 206 31 +test_chromosome 207 31 +test_chromosome 208 32 +test_chromosome 209 31 +test_chromosome 210 31 +test_chromosome 211 31 +test_chromosome 212 31 +test_chromosome 213 31 +test_chromosome 214 31 +test_chromosome 215 31 +test_chromosome 216 30 +test_chromosome 217 28 +test_chromosome 218 28 +test_chromosome 219 27 +test_chromosome 220 27 +test_chromosome 221 28 +test_chromosome 222 28 +test_chromosome 223 28 +test_chromosome 224 28 +test_chromosome 225 29 +test_chromosome 226 29 +test_chromosome 227 30 +test_chromosome 228 30 +test_chromosome 229 31 +test_chromosome 230 30 +test_chromosome 231 31 +test_chromosome 232 32 +test_chromosome 233 33 +test_chromosome 234 34 +test_chromosome 235 33 +test_chromosome 236 33 +test_chromosome 237 32 +test_chromosome 238 32 +test_chromosome 239 32 +test_chromosome 240 30 +test_chromosome 241 30 +test_chromosome 242 29 +test_chromosome 243 31 +test_chromosome 244 32 +test_chromosome 245 30 +test_chromosome 246 29 +test_chromosome 247 29 +test_chromosome 248 29 +test_chromosome 249 29 +test_chromosome 250 28
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/per_base_coverage_outside_features.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,101 @@ +#chr pos coverage +test_chromosome 351 31 +test_chromosome 352 32 +test_chromosome 353 33 +test_chromosome 354 34 +test_chromosome 355 35 +test_chromosome 356 34 +test_chromosome 357 34 +test_chromosome 358 35 +test_chromosome 359 34 +test_chromosome 360 35 +test_chromosome 361 35 +test_chromosome 362 36 +test_chromosome 363 36 +test_chromosome 364 36 +test_chromosome 365 36 +test_chromosome 366 37 +test_chromosome 367 37 +test_chromosome 368 37 +test_chromosome 369 37 +test_chromosome 370 36 +test_chromosome 371 37 +test_chromosome 372 37 +test_chromosome 373 39 +test_chromosome 374 39 +test_chromosome 375 38 +test_chromosome 376 36 +test_chromosome 377 36 +test_chromosome 378 36 +test_chromosome 379 36 +test_chromosome 380 34 +test_chromosome 381 33 +test_chromosome 382 32 +test_chromosome 383 32 +test_chromosome 384 31 +test_chromosome 385 31 +test_chromosome 386 31 +test_chromosome 387 31 +test_chromosome 388 31 +test_chromosome 389 30 +test_chromosome 390 30 +test_chromosome 391 30 +test_chromosome 392 30 +test_chromosome 393 30 +test_chromosome 394 30 +test_chromosome 395 30 +test_chromosome 396 29 +test_chromosome 397 28 +test_chromosome 398 28 +test_chromosome 399 28 +test_chromosome 400 27 +test_chromosome 501 25 +test_chromosome 502 25 +test_chromosome 503 25 +test_chromosome 504 25 +test_chromosome 505 25 +test_chromosome 506 24 +test_chromosome 507 23 +test_chromosome 508 22 +test_chromosome 509 21 +test_chromosome 510 21 +test_chromosome 511 21 +test_chromosome 512 21 +test_chromosome 513 21 +test_chromosome 514 21 +test_chromosome 515 21 +test_chromosome 516 21 +test_chromosome 517 20 +test_chromosome 518 18 +test_chromosome 519 17 +test_chromosome 520 17 +test_chromosome 521 17 +test_chromosome 522 16 +test_chromosome 523 15 +test_chromosome 524 15 +test_chromosome 525 14 +test_chromosome 526 14 +test_chromosome 527 13 +test_chromosome 528 12 +test_chromosome 529 11 +test_chromosome 530 10 +test_chromosome 531 10 +test_chromosome 532 10 +test_chromosome 533 9 +test_chromosome 534 9 +test_chromosome 535 8 +test_chromosome 536 8 +test_chromosome 537 7 +test_chromosome 538 7 +test_chromosome 539 7 +test_chromosome 540 7 +test_chromosome 541 6 +test_chromosome 542 6 +test_chromosome 543 6 +test_chromosome 544 5 +test_chromosome 545 5 +test_chromosome 546 4 +test_chromosome 547 4 +test_chromosome 548 2 +test_chromosome 549 2 +test_chromosome 550 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_counts_custom.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,2 @@ +#GeneID try_this +GENE1 45
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_results_custom.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,48 @@ +RNA-Seq QC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmp_CFvEQ/files/000/dataset_49.dat + gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat + counting algorithm = proportional + protocol = strand-specific-forward + + +>>>>>>> Reads alignment + + reads aligned (left/right) = 0 / 0 + read pairs aligned = 0 + total alignments = 101 + secondary alignments = 1 + non-unique alignments = 0 + aligned to genes = 46 + ambiguous alignments = 0 + no feature assigned = 55 + not aligned = 0 + + +>>>>>>> Reads genomic origin + + exonic = 46 (45.54%) + intronic = 0 (0%) + intergenic = 55 (54.46%) + overlapping exon = 0 (0%) + + +>>>>>>> Transcript coverage profile + + 5' bias = NaN + 3' bias = NaN + 5'-3' bias = NaN + + +>>>>>>> Junction analysis + + reads at junctions = 53 + + CTTT : 47.17% + CCAC : 47.17% + GCAC : 1.89% + CTAC : 1.89% + GAAT : 1.89%
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_results_default.txt Thu Oct 10 17:42:04 2019 -0400 @@ -0,0 +1,47 @@ +RNA-Seq QC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmp_CFvEQ/files/000/dataset_1.dat + gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat + counting algorithm = uniquely-mapped-reads + protocol = non-strand-specific + + +>>>>>>> Reads alignment + + reads aligned = 100 + total alignments = 101 + secondary alignments = 1 + non-unique alignments = 2 + aligned to genes = 54 + ambiguous alignments = 0 + no feature assigned = 45 + not aligned = 0 + SSP estimation (fwd/rev) = 0.59 / 0.41 + + +>>>>>>> Reads genomic origin + + exonic = 54 (54.55%) + intronic = 0 (0%) + intergenic = 45 (45.45%) + overlapping exon = 0 (0%) + + +>>>>>>> Transcript coverage profile + + 5' bias = NaN + 3' bias = NaN + 5'-3' bias = NaN + + +>>>>>>> Junction analysis + + reads at junctions = 52 + + CTTT : 48.08% + CCAC : 48.08% + GCAC : 1.92% + CTAC : 1.92%