Mercurial > repos > iuc > rna_starsolo
changeset 13:9ee34ba73ebf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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--- a/macros.xml Tue Nov 01 16:57:42 2022 +0000 +++ b/macros.xml Fri Feb 17 20:04:43 2023 +0000 @@ -1,11 +1,12 @@ <macros> - <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager - whenever you make changes to the following two version tokens! + <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@ + whenever you make changes to the @TOOL_VERSION@ token! The data manager uses a symlink to this macro file to keep the STAR and - the index versions in sync, but you should manually adjust the +galaxy - version number. --> + the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ --> <!-- STAR version to be used --> - <token name="@VERSION@">2.7.8a</token> + <token name="@TOOL_VERSION@">2.7.10b</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> <!-- STAR index version compatible with this version of STAR This is the STAR version that introduced the index structure expected by the current version. @@ -14,12 +15,14 @@ or by looking for the versionGenome parameter in source/parametersDefault of STAR's source code --> <token name="@IDX_VERSION@">2.7.4a</token> + <token name="@IDX_VERSION_SUFFIX@">1</token> <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">star</requirement> - <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="@TOOL_VERSION@">star</requirement> + <requirement type="package" version="1.16.1">samtools</requirement> + <requirement type="package" version="1.12">gzip</requirement> <yield /> </requirements> </xml> @@ -35,7 +38,7 @@ </xml> <xml name="index_selection" token_with_gene_model="0"> - <param argument="--genomeDir" name="genomeDir" type="select" + <param argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> <options from_data_table="@IDX_DATA_TABLE@"> @@ -55,8 +58,8 @@ <citation type="doi">10.1093/bioinformatics/bts635</citation> </citations> </xml> - <xml name="@SJDBOPTIONS@" token_optional="true"> - <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/> + <xml name="SJDBOPTIONS"> + <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/> <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> </xml> <xml name="dbKeyActions"> @@ -81,11 +84,16 @@ <token name="@TEMPINDEX@"><![CDATA[ ## Create temporary index for custom reference #if str($refGenomeSource.geneSource) == 'history': + #if $refGenomeSource.genomeFastaFiles.ext == "fasta" + ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa && + #else + gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa && + #end if mkdir -p tempstargenomedir && STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' - --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}' + --genomeFastaFiles refgenome.fa ## Handle difference between indices with/without annotations #if 'GTFconditional' in $refGenomeSource: ## GTFconditional exists only in STAR, but not STARsolo @@ -109,6 +117,8 @@ --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases} #end if --runThreadN \${GALAXY_SLOTS:-4} + ## in bytes + --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000)) && #end if ]]></token> @@ -121,17 +131,15 @@ #else: '${refGenomeSource.GTFconditional.genomeDir.fields.path}' ## Handle difference between indices with/without annotations - #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf': - #if $refGenomeSource.GTFconditional.sjdbGTFfile: - --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang - --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' - #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': - --sjdbGTFtagExonParentTranscript Parent - #end if + #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf': + --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang + --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' + #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': + --sjdbGTFtagExonParentTranscript Parent #end if #end if - #end if - ]]></token> + #end if + ]]></token> <token name="@READSHANDLING@" ><![CDATA[ ## Check that the input pairs are of the same type ## otherwise STARsolo will run for a long time and then error out. @@ -161,8 +169,13 @@ @FASTQ_GZ_OPTION@ #end if ]]></token> + <token name="@LIMITS@" ><![CDATA[ + --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000)) + --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000)) + --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000)) + ]]></token> <xml name="ref_selection"> - <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> + <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome" /> <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/> </xml> <xml name="stdio" > @@ -245,4 +258,143 @@ <option value="None" >No adapter clipping</option> </param> </xml> + <xml name="common_SAM_attributes"> + <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option> + <option value="HI" selected="true">HI (query hit index)</option> + <option value="AS" selected="true">AS (local alignment score)</option> + <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option> + <option value="NM">NM (edit distance of the aligned read to the reference)</option> + <option value="MD">MD (string for mismatching positions)</option> + <option value="jM">jM (intron motifs for all junctions)</option> + <option value="jI">jI (1-based start and end of introns for all junctions)</option> + </xml> + <xml name="limits"> + <section name="junction_limits" title="Junction Limits" expanded="false"> + <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" /> + <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" /> + <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." /> + </section> + </xml> + <xml name="outCountActions"> + <actions> + <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> + </actions> + </xml> + <xml name="outWig"> + <conditional name="outWig"> + <param name="outWigType" type="select" label="Compute coverage"> + <option value="None">No coverage</option> + <option value="bedGraph">Yes in bedgraph format</option> + <option value="wiggle">Yes in wiggle format</option> + </param> + <when value="None"> + <!-- This is necessary for the filtering of output --> + <param name="outWigStrand" type="hidden" value="false" /> + </when> + <when value="bedGraph"> + <expand macro="outWigParams"/> + </when> + <when value="wiggle"> + <expand macro="outWigParams"/> + </when> + </conditional> + </xml> + <xml name="outWigParams"> + <param name="outWigTypeSecondWord" type="select" label="Input for coverage"> + <option value="">Default (everything that mapped)</option> + <option value="read_5p">signal from only 5’ of the 1st read</option> + <option value="read2">signal from only 2nd read</option> + </param> + <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="collapse strands (unstranded coverage)" help="By default, the strands are separated."/> + <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/> + <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/> + </xml> + <token name="@OUTWIG@"><![CDATA[ + #if str($outWig.outWigType) != 'None': + --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord' + --outWigStrand '$outWig.outWigStrand' + --outWigReferencesPrefix '$outWig.outWigReferencesPrefix' + --outWigNorm '$outWig.outWigNorm' + #end if + ]]></token> + <token name="@OUTWIGOUTPUTS@"><![CDATA[ + #if str($outWig.outWigType) == "bedGraph": + && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out + && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out + #if str($outWig.outWigStrand) == "Stranded": + && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out + && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out + #end if + #elif str($outWig.outWigType) == "wiggle": + && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out + && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out + #if str($outWig.outWigStrand) == "Stranded": + && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out + && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out + #end if + #end if + ]]></token> + <xml name="outWigOutputs"> + <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out"> + <filter>outWig['outWigType'] != "None"</filter> + <expand macro="dbKeyActions" /> + <change_format> + <when input="outWig.outWigType" value="wiggle" format="wig" /> + </change_format> + </data> + <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out"> + <filter>outWig['outWigType'] != "None"</filter> + <expand macro="dbKeyActions" /> + <change_format> + <when input="outWig.outWigType" value="wiggle" format="wig" /> + </change_format> + </data> + <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out"> + <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter> + <expand macro="dbKeyActions" /> + <change_format> + <when input="outWig.outWigType" value="wiggle" format="wig" /> + </change_format> + </data> + <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out"> + <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter> + <expand macro="dbKeyActions" /> + <change_format> + <when input="outWig.outWigType" value="wiggle" format="wig" /> + </change_format> + </data> + </xml> + <xml name="quantMode"> + <conditional name="quantmode_output"> + <param argument="--quantMode" type="select" + label="Per gene/transcript output" + help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!"> + <option value="-">No per gene or transcript output</option> + <option value="GeneCounts">Per gene read counts (GeneCounts)</option> + <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option> + <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option> + </param> + <when value="-" /> + <when value="GeneCounts" /> + <when value="TranscriptomeSAM"> + <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" + label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" + help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." /> + </when> + <when value="TranscriptomeSAM GeneCounts"> + <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" + label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" + help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." /> + </when> + </conditional> + </xml> + <xml name="quantModeNoGTF"> + <conditional name="quantmode_output"> + <param argument="--quantMode" type="select" + label="Per gene/transcript output"> + <option value="-">No per gene or transcript output as no GTF was provided</option> + </param> + <when value="-" /> + </conditional> + </xml> </macros>
--- a/rg_rnaStarSolo.xml Tue Nov 01 16:57:42 2022 +0000 +++ b/rg_rnaStarSolo.xml Fri Feb 17 20:04:43 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="rna_starsolo" name="RNA STARSolo" version="@VERSION@" profile="20.01" license="MIT"> +<tool id="rna_starsolo" name="RNA STARSolo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description> <macros> <import>macros.xml</import> @@ -22,16 +22,20 @@ #if str($sc.solo_type) == "CB_UMI_Simple": @READSHANDLING@ - --soloCBwhitelist '$sc.soloCBwhitelist' + #if $sc.soloCBwhitelist: + --soloCBwhitelist '$sc.soloCBwhitelist' + #else + --soloCBwhitelist None + #end if ## 1 - check length of barcode, 0 - do not check ## Good for checking custom chemistries --soloBarcodeReadLength $sc.soloBarcodeReadLength - #if str($sc.params.chemistry) == "CR2": + #if str($sc.params.chemistry) == "Cv2": --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 10 - #else if str($sc.params.chemistry) == "CR3": + #else if str($sc.params.chemistry) == "Cv3": --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 @@ -90,12 +94,20 @@ --soloCBwhitelist None #end if - --soloUMIfiltering $solo.soloUMIfiltering --soloStrand $solo.soloStrand --soloFeatures $solo.soloFeatures - --soloUMIdedup $sc.soloUMIdedup - --quantMode TranscriptomeSAM - --outSAMtype BAM Unsorted + --soloUMIdedup $sc.umidedup.soloUMIdedup + #if str($sc.umidedup.soloUMIdedup) == "1MM_CR": + --soloUMIfiltering $sc.umidedup.soloUMIfiltering + #end if + --quantMode TranscriptomeSAM $solo.quantModeGene + #set $tag_names = str($solo.outSAMattributes).replace(',', ' ') + --outSAMattributes $tag_names + #if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != 'None': + --outSAMtype BAM SortedByCoordinate + #else: + --outSAMtype BAM Unsorted + #end if #if str($solo.filter.filter_type) == "cellranger2": --soloCellFilter CellRanger2.2 $solo.filter.n_expected $solo.filter.max_perc $solo.filter.max_min_ratio @@ -109,24 +121,39 @@ ## Splice junctions are always under "raw" directory --soloOutFormatFeaturesGeneField3 '${solo.soloOutFormatFeaturesGeneField3}' + + ## Limits + @LIMITS@ + + ##outWig: + @OUTWIG@ ## Rename the the selected features directory && mv Solo.out/${solo.soloFeatures} Solo.out/soloFeatures ## put the barcodes and features stats into a single file && cat <(echo "Barcodes:") Solo.out/Barcodes.stats <(echo "Genes:") Solo.out/soloFeatures/Features.stats > '${output_stats}' - ## BAM sorting (logic copied from samtools_sort wrapper) - ## choosing BAM SortedByCoord appeared once to give fewer reads - ## than BAM Unsorted followed by a samtools sort - ## so better go with the latter? + + #if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != 'None': + ## recompress BAM output for smaller file size + && samtools view -b -o '$output_BAM' Aligned.sortedByCoord.out.bam + #else: + ## BAM sorting (logic copied from samtools_sort wrapper) + ## choosing BAM SortedByCoord appeared once to give fewer reads + ## than BAM Unsorted followed by a samtools sort + ## so better go with the latter? - && - ##compute the number of ADDITIONAL threads to be used by samtools (-@) - addthreads=\${GALAXY_SLOTS:-2} && (( addthreads-- )) && - ##compute the number of memory available to samtools sort (-m) - ##use only 75% of available: https://github.com/samtools/samtools/issues/831 - addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && - ((addmemory=addmemory*75/100)) && - samtools sort -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" -O bam -o '$output_BAM' Aligned.out.bam + && + ##compute the number of ADDITIONAL threads to be used by samtools (-@) + addthreads=\${GALAXY_SLOTS:-2} && (( addthreads-- )) && + ##compute the number of memory available to samtools sort (-m) + ##use only 75% of available: https://github.com/samtools/samtools/issues/831 + addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && + ((addmemory=addmemory*75/100)) && + samtools sort -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" -O bam -o '$output_BAM' Aligned.out.bam + #end if + ##outWig: + @OUTWIGOUTPUTS@ + ]]></command> <configfiles> <configfile name="manifest_file" > @@ -170,13 +197,13 @@ </when> <when value="without-gtf"> <expand macro="index_selection" with_gene_model="0" /> - <expand macro="@SJDBOPTIONS@" optional="false" /> + <expand macro="SJDBOPTIONS"/> </when> </conditional> </when> <when value="history"> <expand macro="ref_selection" /> - <expand macro="@SJDBOPTIONS@" optional="false"/> + <expand macro="SJDBOPTIONS"/> </when> </conditional> <conditional name="sc" > @@ -187,15 +214,15 @@ </param> <when value="CB_UMI_Simple"> <expand macro="input_selection" /> - <param format="txt,tsv" argument="--soloCBwhitelist" type="data" label="RNA-Seq Cell Barcode Whitelist"/> + <param format="txt,tsv" argument="--soloCBwhitelist" optional="True" type="data" label="RNA-Seq Cell Barcode Whitelist"/> <conditional name="params" > <param name="chemistry" type="select" label="Configure Chemistry Options"> - <option value="CR2" selected="true">Cell Ranger v2</option> - <option value="CR3">Cell Ranger v3</option> + <option value="Cv2" selected="true">Chromium chemistry v2</option> + <option value="Cv3">Chromium chemistry v3</option> <option value="custom">Custom</option> </param> - <when value="CR2" /> - <when value="CR3" /> + <when value="Cv2" /> + <when value="Cv3" /> <when value="custom" > <param argument="--soloCBstart" type="integer" min="1" value="1" label="Cell Barcode Start Base" /> <param argument="--soloCBlen" type="integer" min="1" value="16" label="Cell Barcode Length" /> @@ -219,11 +246,25 @@ </when> </conditional> <param argument="--soloBarcodeReadLength" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Barcode Size is same size of the Read" help="Disable this if your R1 barcodes contain poly-T bases after the barcode sequence." /> - <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs."> - <expand macro="umidedup_options" /> - <option value="Exact" >Exact</option> - <option value="1MM_CR" >CellRanger2-4 algorithm</option> - </param> + <conditional name="umidedup"> + <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs."> + <expand macro="umidedup_options" /> + <option value="Exact" >Exact</option> + <option value="1MM_CR" >CellRanger2-4 algorithm</option> + </param> + <when value="1MM_All"/> + <when value="1MM_Directional_UMItools"/> + <when value="1MM_Directional"/> + <when value="Exact"/> + <when value="1MM_CR"> + <param argument="--soloUMIfiltering" type="select" label="Type of UMI filtering" > + <option value="-" selected="true">Remove UMIs with N and homopolymers (similar to CellRanger 2.2.0)</option> + <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option> + <option value="MultiGeneUMI_All" >Remove all UMIs that map to more than one gene</option> + <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option> + </param> + </when> + </conditional> <param argument="--soloCBmatchWLtype" type="select" label="Matching the Cell Barcodes to the WhiteList" help="Exact: only exact matches allowed; 1MM: only one match in whitelist with 1 mismatched base allowed. Allowed CBs have to have at least one read with exact match; 1MM_multi: multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches; 1MM_multi_pseudocounts: same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes."> <expand macro="cb_match_wl_common" /> @@ -252,23 +293,46 @@ </param> <param name="umi_end_anchor_pos" type="integer" value="0" label="0-based position of the UMI end with respect to the anchor base" /> <expand macro="solo_adapter_params" /> - <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs."> - <expand macro="umidedup_options" /> - <option value="Exact" >Exact</option> - <option value="1MM_CR" >CellRanger2-4 algorithm</option> - </param> + <conditional name="umidedup"> + <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs."> + <expand macro="umidedup_options" /> + <option value="Exact" >Exact</option> + <option value="1MM_CR" >CellRanger2-4 algorithm</option> + </param> + <when value="1MM_All"/> + <when value="1MM_Directional_UMItools"/> + <when value="1MM_Directional"/> + <when value="Exact"/> + <when value="1MM_CR"> + <param argument="--soloUMIfiltering" type="select" label="Type of UMI filtering" > + <option value="-" selected="true">Remove UMIs with N and homopolymers (similar to CellRanger 2.2.0)</option> + <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option> + <option value="MultiGeneUMI_All" >Remove all UMIs that map to more than one gene</option> + <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option> + </param> + </when> + </conditional> <param argument="--soloCBmatchWLtype" type="select" label="Matching the Cell Barcodes to the WhiteList" help="Exact: only exact matches allowed; 1MM: only one match in whitelist with 1 mismatched base allowed. Allowed CBs have to have at least one read with exact match; 1MM_multi: multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches; 1MM_multi_pseudocounts: same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes."> <expand macro="cb_match_wl_common" /> + <!-- should we add EditDist_2? --> </param> </when> <when value="SmartSeq"> <expand macro="input_selection_smart_seq" /> <param name="cell_ids" format="txt,tsv" type="data" label="File containing cell IDs of the samples. One ID per line in order of samples in the above collection."/> - <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs."> - <option value="Exact" >Exact</option> - <option value="NoDedup">Do not deduplicate UMIs</option> - </param> + <conditional name="umidedup"> + <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs."> + <expand macro="umidedup_options" /> + <option value="Exact" >Exact</option> + <option value="NoDedup" >CellRanger2-4 algorithm</option> + </param> + <when value="1MM_All"/> + <when value="1MM_Directional_UMItools"/> + <when value="1MM_Directional"/> + <when value="Exact"/> + <when value="NoDedup"/> + </conditional> </when> </conditional> <section name="solo" title="Advanced Settings" expanded="true"> @@ -281,11 +345,8 @@ <option value="Gene" selected="true">Gene: Count reads matching the Gene Transcript</option> <option value="SJ" >Splice Junctions: Count reads at exon-intron junctions</option> <option value="GeneFull" >Full: Count all reads overlapping genes' exons and introns</option> - </param> - <param argument="--soloUMIfiltering" type="select" label="Type of UMI filtering" > - <option value="-" selected="true">Remove UMIs with N and homopolymers (similar to CellRanger 2.2.0)</option> - <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option> - <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option> + <option value="GeneFull_ExonOverIntron" >Full: Count all reads overlapping genes' exons and introns: prioritize 100% overlap with exons</option> + <option value="GeneFull_Ex50pAS" >Full: Count all reads overlapping genes' exons and introns: prioritize 50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.</option> </param> <conditional name="filter" > <param name="filter_type" type="select" label="Cell filtering type and parameters" > @@ -298,6 +359,7 @@ <param name="n_expected" type="integer" min="1" value="3000" label="Number of expected cells" /> <param name="max_perc" type="float" min="0" max="1" value="0.99" label="Robust maximum percentile for UMI count" /> <param name="max_min_ratio" type="float" min="1" value="10" label="Maximum to minimum ratio for UMI count" /> + <param name="output_raw" type="boolean" checked="false" label="Output raw matrix in addition to filtered one" /> </when> <when value="emptydrops" > <param name="nExpectedCells" type="integer" min="1" value="3000" label="Number of expected cells" /> @@ -310,14 +372,31 @@ <param name="candMaxN" type="integer" value="20000" label="Number of extra barcodes after initial cell calling" /> <param name="FDR" type="float" value="0.01" label="Maximum adjusted p-value for determining a barcode as non-ambient" /> <param name="simN" type="integer" value="10000" label="Number of log likelihood simulations" /> + <param name="output_raw" type="boolean" checked="false" label="Output raw matrix in addition to filtered one" /> </when> <when value="topcells" > <param name="n_cells" type="integer" min="1" value="3000" label="Number of top cells to report sorted by UMI count" /> + <param name="output_raw" type="boolean" checked="false" label="Output raw matrix in addition to filtered one" /> </when> - <when value="no_filter" /> + <when value="no_filter"> + <param name="output_raw" type="hidden" value="true" /> + </when> </conditional> <param argument="--soloOutFormatFeaturesGeneField3" type="text" value="Gene Expression" label="Field 3 in the Genes output." help="Input '-' to remove the 3rd column from the output." /> + <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true" + label="Read alignment tags to include in the BAM output"> + <expand macro="common_SAM_attributes"/> + <option value="CR">CR Cellular barcode sequence bases (uncorrected)</option> + <option value="CY">CY Phred quality of the cellular barcode sequence in the CR tag</option> + <option value="GX">GX Gene ID</option> + <option value="GN">GN Gene name</option> + <option value="CB">CB Cell identifier (corrected)</option> + <option value="UB">UB UMI (corrected)</option> + </param> + <param name="quantModeGene" type="boolean" truevalue="GeneCounts" falsevalue="" checked="false" label="Output global gene count" help="Can be used by MultiQC" /> + <expand macro="limits" /> </section> + <expand macro="outWig"/> </inputs> <outputs> <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"> @@ -333,7 +412,7 @@ <!-- soloCellFilter set to None, if SJ is selected for soloFeatures --> <data format="tsv" name="output_genes" label="${tool.name} on ${on_string}: Genes raw" from_work_dir="Solo.out/soloFeatures/raw/features.tsv" > - <filter>solo['filter']['filter_type'] == "no_filter" or solo['soloFeatures'] == "SJ" </filter> + <filter>solo['filter']['output_raw'] or solo['soloFeatures'] == "SJ" </filter> </data> <data format="tsv" name="output_genes_filtered" label="${tool.name} on ${on_string}: Genes filtered" from_work_dir="Solo.out/soloFeatures/filtered/features.tsv" > @@ -341,7 +420,7 @@ </data> <data format="tsv" name="output_barcodes" label="${tool.name} on ${on_string}: Barcodes raw" from_work_dir="Solo.out/soloFeatures/raw/barcodes.tsv" > - <filter>solo['filter']['filter_type'] == "no_filter" or solo['soloFeatures'] == "SJ" </filter> + <filter>solo['filter']['output_raw'] or solo['soloFeatures'] == "SJ" </filter> </data> <data format="tsv" name="output_barcodes_filtered" label="${tool.name} on ${on_string}: Barcodes filtered" from_work_dir="Solo.out/soloFeatures/filtered/barcodes.tsv" > @@ -349,7 +428,7 @@ </data> <data format="mtx" name="output_matrix" label="${tool.name} on ${on_string}: Matrix Gene Counts raw" from_work_dir="Solo.out/soloFeatures/raw/matrix.mtx" > - <filter>solo['soloFeatures'] == "Gene" and solo['filter']['filter_type'] == "no_filter" </filter> + <filter>solo['soloFeatures'] == "Gene" and solo['filter']['output_raw'] </filter> <expand macro="dbKeyActions" /> </data> <data format="mtx" name="output_matrix_filtered" label="${tool.name} on ${on_string}: Matrix Gene Counts filtered" @@ -364,18 +443,24 @@ </data> <data format="mtx" name="output_matrixGeneFull" label="${tool.name} on ${on_string}: Matrix Full Gene Counts raw" from_work_dir="Solo.out/soloFeatures/raw/matrix.mtx" > - <filter>solo['soloFeatures'] == "GeneFull" and solo['filter']['filter_type'] == "no_filter" </filter> + <filter>"GeneFull" in solo['soloFeatures'] and solo['filter']['output_raw'] </filter> <expand macro="dbKeyActions" /> </data> <data format="mtx" name="output_matrixGeneFull_filtered" label="${tool.name} on ${on_string}: Matrix Full Gene Counts filtered" from_work_dir="Solo.out/soloFeatures/filtered/matrix.mtx" > - <filter>solo['soloFeatures'] == "GeneFull" and solo['filter']['filter_type'] != "no_filter" </filter> + <filter>"GeneFull" in solo['soloFeatures'] and solo['filter']['filter_type'] != "no_filter" </filter> <expand macro="dbKeyActions" /> </data> <data format="bam" name="output_BAM" label="${tool.name} on ${on_string}: Alignments" > <expand macro="dbKeyActions" /> </data> <data format="txt" name="output_stats" label="${tool.name} on ${on_string}: Barcode/Feature Statistic Summaries"/> + <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: combined reads per gene" from_work_dir="ReadsPerGene.out.tab"> + <filter>solo['quantModeGene']</filter> + <expand macro="dbKeyActions" /> + <expand macro="outCountActions" /> + </data> + <expand macro="outWigOutputs"/> </outputs> <!-- Generating test data that is big enough for STARsolo to detect and small enough for Galaxy to test requires careful modification of input FASTA and GTF data, @@ -386,7 +471,8 @@ here: https://gist.github.com/mtekman/149a7c52fd73e5d8ebe49f5a27b0743d --> <tests> - <test expect_num_outputs="6"> + <test expect_num_outputs="7"> + <!-- test 1 --> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> @@ -403,9 +489,11 @@ </conditional> <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> <conditional name="params"> - <param name="chemistry" value="CR3" /> + <param name="chemistry" value="Cv3" /> </conditional> - <param name="soloUMIdedup" value="1MM_All" /> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_All" /> + </conditional> </conditional> <section name="solo" > <conditional name="filter"> @@ -413,35 +501,47 @@ </conditional> <param name="soloStrand" value="Forward" /> <param name="soloFeatures" value="Gene" /> + <param name="quantModeGene" value="true" /> </section> <output name="output_barcodes" > <assert_contents> <!-- first and last line --> <has_line line="AAACCTGAGCGCTCCA" /> <has_line line="TTTGGTTAGTGGGCTA" /> + <has_n_lines n="394" /> </assert_contents> </output> <output name="output_genes"> <assert_contents> <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" /> <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" /> + <has_n_lines n="14" /> </assert_contents> </output> <output name="output_matrix" > <assert_contents> <has_line_matching expression="14\s+394\s+7" /> <has_line_matching expression="4\s+381\s+1" /> + <has_n_lines n="10" /> </assert_contents> </output> <output name="output_stats" > <assert_contents> - <has_line_matching expression="\s+nUnmapped\s+5823" /> - <has_line_matching expression="\s+nUMIs\s+8" /> + <has_line_matching expression="\s+noUnmapped\s+5823" /> + <has_line_matching expression="\s+yesUMIs\s+8" /> </assert_contents> </output> <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" /> + <output name="reads_per_gene" > + <assert_contents> + <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" /> + <has_line_matching expression="ENSG00000275464\s+38\s+1\s+40" /> + </assert_contents> + </output> </test> - <test expect_num_outputs="6"><!-- same as above, but using custom --> + <test expect_num_outputs="6"> + <!-- test 2 --> + <!-- same as above, but using custom and no reads_per_gene--> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> @@ -471,31 +571,37 @@ </section> <output name="output_barcodes_filtered" > <assert_contents> + <!-- first and last line --> <has_line line="ACACCGGTCTAACGGT" /> <has_line line="TTCTCAATCCACGTTC" /> + <has_n_lines n="7" /> </assert_contents> </output> <output name="output_genes_filtered"> <assert_contents> <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" /> <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" /> + <has_n_lines n="14" /> </assert_contents> </output> <output name="output_matrix_filtered" > <assert_contents> <has_line_matching expression="14\s+7\s+7" /> <has_line_matching expression="4\s+7\s+1" /> + <has_n_lines n="10" /> </assert_contents> </output> <output name="output_stats" > <assert_contents> - <has_line_matching expression="\s+nUnmapped\s+5823" /> - <has_line_matching expression="\s+nUMIs\s+8" /> + <has_line_matching expression="\s+noUnmapped\s+5823" /> + <has_line_matching expression="\s+yesUMIs\s+8" /> </assert_contents> </output> <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" /> </test> - <test expect_num_outputs="6"><!-- Multiple repeats test --> + <test expect_num_outputs="6"> + <!-- test 3 --> + <!-- Multiple repeats test --> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> @@ -512,9 +618,11 @@ </conditional> <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> <conditional name="params"> - <param name="chemistry" value="CR3" /> + <param name="chemistry" value="Cv3" /> </conditional> - <param name="soloUMIdedup" value="1MM_All" /> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_All" /> + </conditional> </conditional> <section name="solo" > <param name="soloStrand" value="Forward" /> @@ -524,11 +632,17 @@ <assert_contents> <has_line line="ACACCGGTCTAACGGT" /> <has_line line="TTCTCAATCCACGTTC" /> + <has_n_lines n="7" /> </assert_contents> </output> - <!-- BAM output is huge, we don't need to test here --> + <output name="output_BAM" > + <assert_contents> + <has_size value="166147" delta="600" /> + </assert_contents> + </output> </test> - <test expect_num_outputs="6"> + <test expect_num_outputs="10"> + <!-- test 4 --> <!-- Test with paired collection --> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> @@ -550,24 +664,35 @@ </conditional> <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> <conditional name="params"> - <param name="chemistry" value="CR3" /> + <param name="chemistry" value="Cv3" /> </conditional> - <param name="soloUMIdedup" value="1MM_All" /> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_All" /> + </conditional> </conditional> <section name="solo" > <param name="soloStrand" value="Forward" /> <param name="soloFeatures" value="Gene" /> </section> + <conditional name="outWig"> + <param name="outWigType" value="bedGraph" /> + </conditional> <output name="output_barcodes_filtered" > <assert_contents> <has_line line="ACACCGGTCTAACGGT" /> <has_line line="TTCTCAATCCACGTTC" /> + <has_n_lines n="7" /> </assert_contents> </output> <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" /> + <output name="signal_unique_str1" file="Signal.Unique.str1.out.bg" /> + <output name="signal_uniquemultiple_str1" file="Signal.UniqueMultiple.str1.out.bg" /> + <output name="signal_unique_str2" file="Signal.Unique.str2.out.bg" /> + <output name="signal_uniquemultiple_str2" file="Signal.UniqueMultiple.str2.out.bg" /> </test> - <test expect_num_outputs="6"> - <!-- Test soloFeatures, soloCBmatchWLtype, soloCellFilter, soloOutFormatFeaturesGeneField3, soloUMIfiltering --> + <test expect_num_outputs="9"> + <!-- test 5 --> + <!-- Test soloFeatures, soloCBmatchWLtype, soloCellFilter, soloOutFormatFeaturesGeneField3 --> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> @@ -585,17 +710,19 @@ <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> <param name="soloCBmatchWLtype" value="1MM_multi_pseudocounts" /> <conditional name="params"> - <param name="chemistry" value="CR3" /> + <param name="chemistry" value="Cv3" /> </conditional> - <param name="soloUMIdedup" value="1MM_All" /> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_All" /> + </conditional> </conditional> <section name="solo" > - <param name="soloUMIfiltering" value="MultiGeneUMI" /> <param name="soloStrand" value="Forward" /> <param name="soloFeatures" value="GeneFull" /> <conditional name="filter"> <param name="filter_type" value="topcells" /> <param name="n_cells" value="5" /> + <param name="output_raw" value="true" /> </conditional> <param name="soloOutFormatFeaturesGeneField3" value="Dummy Text" /> </section> @@ -604,22 +731,48 @@ <!-- first and last line --> <has_line line="AGACGTTCAAGGCTCC" /> <has_line line="TCAACGAAGCTAGTGG" /> + <has_n_lines n="6" /> </assert_contents> </output> <output name="output_genes_filtered" > <assert_contents> <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Dummy\s+Text" /> <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Dummy\s+Text" /> + <has_n_lines n="14" /> </assert_contents> </output> <output name="output_matrixGeneFull_filtered" > <assert_contents> <has_line_matching expression="14\s+6\s+14" /> <has_line_matching expression="10\s+6\s+1" /> + <has_n_lines n="17" /> + </assert_contents> + </output> + <output name="output_barcodes" > + <assert_contents> + <!-- first and last line --> + <has_line line="AAACCTGAGCGCTCCA" /> + <has_line line="TTTGGTTAGTGGGCTA" /> + <has_n_lines n="394" /> + </assert_contents> + </output> + <output name="output_genes"> + <assert_contents> + <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Dummy\s+Text" /> + <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Dummy\s+Text" /> + <has_n_lines n="14" /> + </assert_contents> + </output> + <output name="output_matrix" > + <assert_contents> + <has_line_matching expression="14\s+394\s+195" /> + <has_line_matching expression="3\s+1\s+1" /> + <has_n_lines n="198" /> </assert_contents> </output> </test> <test expect_num_outputs="6"> + <!-- test 6 --> <!-- Emptydrops filtering --> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> @@ -637,9 +790,11 @@ </conditional> <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> <conditional name="params"> - <param name="chemistry" value="CR3" /> + <param name="chemistry" value="Cv3" /> </conditional> - <param name="soloUMIdedup" value="1MM_All" /> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_All" /> + </conditional> </conditional> <section name="solo" > <conditional name="filter"> @@ -663,29 +818,33 @@ <!-- first and last line --> <has_line line="ACACCGGTCTAACGGT" /> <has_line line="TTCTCAATCCACGTTC" /> + <has_n_lines n="7" /> </assert_contents> </output> <output name="output_genes_filtered"> <assert_contents> <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" /> <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" /> + <has_n_lines n="14" /> </assert_contents> </output> <output name="output_matrix_filtered" > <assert_contents> <has_line_matching expression="14\s+7\s+7" /> <has_line_matching expression="4\s+7\s+1" /> + <has_n_lines n="10" /> </assert_contents> </output> <output name="output_stats" > <assert_contents> - <has_line_matching expression="\s+nUnmapped\s+5823" /> - <has_line_matching expression="\s+nUMIs\s+8" /> + <has_line_matching expression="\s+noUnmapped\s+5823" /> + <has_line_matching expression="\s+yesUMIs\s+8" /> </assert_contents> </output> <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" /> </test> <test expect_num_outputs="6"> + <!-- test 7 --> <!-- Test soloType CB_UMI_Complex --> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> @@ -722,7 +881,9 @@ <param name="soloAdapterSequence" value="GAGTGATTGCTTGTGACGCCTT" /> <param name="soloAdapterMismatchesNmax" value="1" /> <param name="clipAdapterType" value="CellRanger4" /> - <param name="soloUMIdedup" value="1MM_All" /> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_All" /> + </conditional> <param name="soloCBmatchWLtype" value="1MM" /> </conditional> <output name="output_barcodes_filtered" > @@ -730,28 +891,32 @@ <!-- first and last line --> <has_line line="ACAACGTGG_AAACCTCC" /> <has_line line="ATTCCAGAC_TTCGCTGG" /> + <has_n_lines n="33" /> </assert_contents> </output> <output name="output_genes_filtered"> <assert_contents> <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" /> <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" /> + <has_n_lines n="14" /> </assert_contents> </output> <output name="output_matrix_filtered" > <assert_contents> <has_line_matching expression="14\s+33\s+36" /> <has_line_matching expression="2\s+33\s+1" /> + <has_n_lines n="39" /> </assert_contents> </output> <output name="output_stats" > <assert_contents> - <has_line_matching expression="\s+nExactMatch\s+791" /> - <has_line_matching expression="\s+nUMIs\s+36" /> + <has_line_matching expression="\s+yesWLmatchExact\s+791" /> + <has_line_matching expression="\s+yesUMIs\s+36" /> </assert_contents> </output> </test> <test expect_num_outputs="6"> + <!-- test 8 --> <!-- Test soloType SmartSeq --> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> @@ -824,7 +989,9 @@ </param> </conditional> <param name="cell_ids" value="smartseq.cellids.txt" /> - <param name="soloUMIdedup" value="Exact" /> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="Exact" /> + </conditional> </conditional> <section name="solo" > <param name="soloStrand" value="Unstranded" /> @@ -837,24 +1004,152 @@ <assert_contents> <has_line line="CSC6_D02" /> <not_has_text text="MGH26_A02" /> + <has_n_lines n="3" /> </assert_contents> </output> <output name="output_genes_filtered"> <assert_contents> <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" /> <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" /> + <has_n_lines n="14" /> </assert_contents> </output> <output name="output_matrix_filtered" > <assert_contents> <has_line_matching expression="14\s+3\s+10" /> <has_line_matching expression="12\s+3\s+1" /> + <has_n_lines n="13" /> </assert_contents> </output> <output name="output_stats" > <assert_contents> - <has_line_matching expression="\s+nExactMatch\s+9000" /> - <has_line_matching expression="\s+nUMIs\s+32" /> + <has_line_matching expression="\s+yesWLmatchExact\s+9000" /> + <has_line_matching expression="\s+yesUMIs\s+32" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="6"> + <!-- test 9 --> + <!-- Test outSAMattributes --> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> + <param name="genomeSAindexNbases" value="4" /> + <param name="sjdbOverhang" value="100" /> + <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/> + </conditional> + <conditional name="sc" > + <param name="solo_type" value="CB_UMI_Simple" /> + <conditional name="input_types"> + <param name="use" value="repeat" /> + <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" /> + </conditional> + <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> + <conditional name="params"> + <param name="chemistry" value="Cv3" /> + </conditional> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_All" /> + </conditional> + </conditional> + <section name="solo" > + <conditional name="filter"> + <param name="filter_type" value="no_filter" /> + </conditional> + <param name="soloStrand" value="Forward" /> + <param name="soloFeatures" value="Gene" /> + <param name="outSAMattributes" value="NH,HI,AS,nM,GX,GN,CB,UB" /> + </section> + <output name="output_barcodes" > + <assert_contents> + <!-- first and last line --> + <has_line line="AAACCTGAGCGCTCCA" /> + <has_line line="TTTGGTTAGTGGGCTA" /> + <has_n_lines n="394" /> + </assert_contents> + </output> + <output name="output_genes"> + <assert_contents> + <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" /> + <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" /> + <has_n_lines n="14" /> + </assert_contents> + </output> + <output name="output_matrix" > + <assert_contents> + <has_line_matching expression="14\s+394\s+7" /> + <has_line_matching expression="4\s+381\s+1" /> + <has_n_lines n="10" /> + </assert_contents> + </output> + <output name="output_stats" > + <assert_contents> + <has_line_matching expression="\s+noUnmapped\s+5823" /> + <has_line_matching expression="\s+yesUMIs\s+8" /> + </assert_contents> + </output> + <output name="output_BAM" > + <assert_contents> + <has_size value="153108" delta="600" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="6"> + <!-- test 10 --> + <!-- Test soloFeatures --> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> + <param name="genomeSAindexNbases" value="4" /> + <param name="sjdbOverhang" value="100" /> + <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/> + </conditional> + <conditional name="sc" > + <param name="solo_type" value="CB_UMI_Simple" /> + <conditional name="input_types"> + <param name="use" value="repeat" /> + <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" /> + </conditional> + <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> + <param name="soloCBmatchWLtype" value="1MM_multi_pseudocounts" /> + <conditional name="params"> + <param name="chemistry" value="Cv3" /> + </conditional> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_CR" /> + <param name="soloUMIfiltering" value="MultiGeneUMI" /> + </conditional> + </conditional> + <section name="solo" > + <param name="soloStrand" value="Forward" /> + <param name="soloFeatures" value="GeneFull_ExonOverIntron" /> + <conditional name="filter"> + <param name="filter_type" value="no_filter" /> + </conditional> + <param name="soloOutFormatFeaturesGeneField3" value="Dummy Text" /> + </section> + <output name="output_barcodes" > + <assert_contents> + <!-- first and last line --> + <has_line line="AAACCTGAGCGCTCCA" /> + <has_line line="TTTGGTTAGTGGGCTA" /> + <has_n_lines n="394" /> + </assert_contents> + </output> + <output name="output_genes" > + <assert_contents> + <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Dummy\s+Text" /> + <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Dummy\s+Text" /> + <has_n_lines n="14" /> + </assert_contents> + </output> + <output name="output_matrixGeneFull" > + <assert_contents> + <has_line_matching expression="14\s+394\s+104" /> + <has_line_matching expression="10\s+2\s+1" /> + <has_n_lines n="107" /> </assert_contents> </output> </test>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_splicejunctions_PE.bed Fri Feb 17 20:04:43 2023 +0000 @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 51 0 37 +test_chromosome 401 500 1 1 0 41 0 36
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_Signal.Unique.both.read2.out.wig Fri Feb 17 20:04:43 2023 +0000 @@ -0,0 +1,290 @@ +variableStep chrom=test_chromosome +59 5263.15789 +60 10526.31579 +61 10526.31579 +62 10526.31579 +63 10526.31579 +64 10526.31579 +65 10526.31579 +66 15789.47368 +67 15789.47368 +68 15789.47368 +69 15789.47368 +70 15789.47368 +71 21052.63158 +72 21052.63158 +73 26315.78947 +74 26315.78947 +75 26315.78947 +76 31578.94737 +77 31578.94737 +78 31578.94737 +79 31578.94737 +80 36842.10526 +81 36842.10526 +82 36842.10526 +83 36842.10526 +84 36842.10526 +85 36842.10526 +86 36842.10526 +87 36842.10526 +88 42105.26316 +89 42105.26316 +90 42105.26316 +91 42105.26316 +92 42105.26316 +93 42105.26316 +94 47368.42105 +95 47368.42105 +96 52631.57895 +97 52631.57895 +98 57894.73684 +99 57894.73684 +100 63157.89474 +101 68421.05263 +102 68421.05263 +103 73684.21053 +104 73684.21053 +105 73684.21053 +106 73684.21053 +107 73684.21053 +108 89473.68421 +109 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_rev_Signal.Unique.str2.out.bg Fri Feb 17 20:04:43 2023 +0000 @@ -0,0 +1,124 @@ +test_chromosome 58 59 10416.66667 +test_chromosome 59 65 20833.33333 +test_chromosome 65 70 31250.00000 +test_chromosome 70 72 41666.66667 +test_chromosome 72 75 52083.33333 +test_chromosome 75 79 62500.00000 +test_chromosome 79 87 72916.66667 +test_chromosome 87 93 83333.33333 +test_chromosome 93 95 93750.00000 +test_chromosome 95 97 104166.66667 +test_chromosome 97 99 114583.33333 +test_chromosome 99 100 125000.00000 +test_chromosome 100 102 135416.66667 +test_chromosome 102 107 145833.33333 +test_chromosome 107 112 177083.33333 +test_chromosome 112 118 187500.00000 +test_chromosome 118 121 197916.66667 +test_chromosome 121 128 218750.00000 +test_chromosome 128 130 229166.66667 +test_chromosome 130 131 260416.66667 +test_chromosome 131 132 270833.33333 +test_chromosome 132 133 260416.66667 +test_chromosome 133 136 250000.00000 +test_chromosome 136 137 270833.33333 +test_chromosome 137 138 281250.00000 +test_chromosome 138 140 302083.33333 +test_chromosome 140 145 291666.66667 +test_chromosome 145 147 281250.00000 +test_chromosome 147 150 270833.33333 +test_chromosome 150 152 260416.66667 +test_chromosome 152 153 270833.33333 +test_chromosome 153 154 291666.66667 +test_chromosome 154 155 312500.00000 +test_chromosome 155 156 322916.66667 +test_chromosome 156 159 333333.33333 +test_chromosome 159 160 343750.00000 +test_chromosome 160 161 354166.66667 +test_chromosome 161 163 364583.33333 +test_chromosome 163 164 375000.00000 +test_chromosome 164 165 385416.66667 +test_chromosome 165 167 406250.00000 +test_chromosome 167 168 416666.66667 +test_chromosome 168 169 406250.00000 +test_chromosome 169 171 427083.33333 +test_chromosome 171 172 437500.00000 +test_chromosome 172 177 427083.33333 +test_chromosome 177 182 416666.66667 +test_chromosome 182 183 385416.66667 +test_chromosome 183 187 395833.33333 +test_chromosome 187 194 385416.66667 +test_chromosome 194 196 395833.33333 +test_chromosome 196 199 385416.66667 +test_chromosome 199 200 406250.00000 +test_chromosome 200 204 416666.66667 +test_chromosome 204 205 427083.33333 +test_chromosome 205 207 406250.00000 +test_chromosome 207 209 416666.66667 +test_chromosome 209 211 427083.33333 +test_chromosome 211 212 406250.00000 +test_chromosome 212 213 385416.66667 +test_chromosome 213 220 375000.00000 +test_chromosome 220 224 385416.66667 +test_chromosome 224 226 395833.33333 +test_chromosome 226 227 406250.00000 +test_chromosome 227 228 395833.33333 +test_chromosome 228 229 385416.66667 +test_chromosome 229 232 354166.66667 +test_chromosome 232 233 364583.33333 +test_chromosome 233 234 375000.00000 +test_chromosome 234 235 364583.33333 +test_chromosome 235 236 343750.00000 +test_chromosome 236 238 333333.33333 +test_chromosome 238 239 322916.66667 +test_chromosome 239 240 312500.00000 +test_chromosome 240 242 291666.66667 +test_chromosome 242 243 302083.33333 +test_chromosome 243 244 312500.00000 +test_chromosome 244 245 291666.66667 +test_chromosome 245 246 281250.00000 +test_chromosome 246 249 270833.33333 +test_chromosome 249 250 260416.66667 +test_chromosome 350 351 291666.66667 +test_chromosome 351 352 302083.33333 +test_chromosome 352 353 312500.00000 +test_chromosome 353 354 322916.66667 +test_chromosome 354 357 333333.33333 +test_chromosome 357 358 343750.00000 +test_chromosome 358 359 333333.33333 +test_chromosome 359 361 343750.00000 +test_chromosome 361 365 354166.66667 +test_chromosome 365 369 364583.33333 +test_chromosome 369 370 343750.00000 +test_chromosome 370 372 354166.66667 +test_chromosome 372 374 375000.00000 +test_chromosome 374 379 354166.66667 +test_chromosome 379 380 333333.33333 +test_chromosome 380 381 322916.66667 +test_chromosome 381 383 312500.00000 +test_chromosome 383 395 302083.33333 +test_chromosome 395 399 291666.66667 +test_chromosome 399 400 281250.00000 +test_chromosome 500 505 260416.66667 +test_chromosome 505 506 250000.00000 +test_chromosome 506 507 239583.33333 +test_chromosome 507 508 229166.66667 +test_chromosome 508 516 218750.00000 +test_chromosome 516 517 208333.33333 +test_chromosome 517 518 187500.00000 +test_chromosome 518 521 177083.33333 +test_chromosome 521 522 166666.66667 +test_chromosome 522 524 156250.00000 +test_chromosome 524 526 145833.33333 +test_chromosome 526 527 135416.66667 +test_chromosome 527 528 125000.00000 +test_chromosome 528 529 114583.33333 +test_chromosome 529 532 104166.66667 +test_chromosome 532 534 93750.00000 +test_chromosome 534 536 83333.33333 +test_chromosome 536 540 72916.66667 +test_chromosome 540 543 62500.00000 +test_chromosome 543 545 52083.33333 +test_chromosome 545 547 41666.66667 +test_chromosome 547 549 20833.33333 +test_chromosome 549 550 10416.66667
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_revlib_R1.fastqsanger Fri Feb 17 20:04:43 2023 +0000 @@ -0,0 +1,192 @@ +@test_mRNA_150_290_0/1 +TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_255_2/1 +GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_72_258_4/1 +GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_107_286_5/1 +AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_122_299_6/1 +CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_234_7/1 +AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_155_9/1 +TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_230_b/1 +TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_276_c/1 +CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_268_d/1 +CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_118_297_f/1 +AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_16_194_10/1 +TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_266_13/1 +AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_218_16/1 +AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_195_17/1 +ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_126_282_18/1 +AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_274_1c/1 +TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_225_1e/1 +CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_249_20/1 +GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_267_22/1 +CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_69_229_23/1 +ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_21_208_24/1 +GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_146_27/1 +ACCTACTGCACTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGCATCTGACGCTCTAAGTCCGTCCGTAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_103_284_2a/1 +AAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_271_2b/1 +ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCTGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_50_224_2d/1 +CGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_26_189_30/1 +AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_79_256_31/1 +AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_267_32/1 +CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_145_300_37/1 +GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_228_3a/1 +CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_30_231_3c/1 +CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_220_3d/1 +GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_278_3e/1 +CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_23_186_42/1 +TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_106_253_45/1 +AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_47/1 +TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_63_229_4c/1 +ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_245_4d/1 +CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_88_257_50/1 +TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_9_179_52/1 +TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_250_57/1 +AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_272_5a/1 +GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_114_277_5b/1 +GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_279_5f/1 +CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_293_60/1 +CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_297_61/1 +AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_295_63/1 +TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_revlib_R2.fastqsanger Fri Feb 17 20:04:43 2023 +0000 @@ -0,0 +1,192 @@ +@test_mRNA_150_290_0/2 +TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_255_2/2 +GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_72_258_4/2 +ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_107_286_5/2 +TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_122_299_6/2 +GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_234_7/2 +GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_155_9/2 +TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_230_b/2 +AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_276_c/2 +ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_268_d/2 +CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_118_297_f/2 +GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_16_194_10/2 +GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_266_13/2 +ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_218_16/2 +GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_195_17/2 +GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_126_282_18/2 +GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_274_1c/2 +GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_225_1e/2 +ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_249_20/2 +GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_267_22/2 +ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_69_229_23/2 +AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_21_208_24/2 +GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_146_27/2 +GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_103_284_2a/2 +CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_271_2b/2 +TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_50_224_2d/2 +CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_26_189_30/2 +GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_79_256_31/2 +ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_267_32/2 +AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_145_300_37/2 +GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_228_3a/2 +GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_30_231_3c/2 +GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_220_3d/2 +GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_278_3e/2 +GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_23_186_42/2 +GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_106_253_45/2 +CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_47/2 +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_63_229_4c/2 +ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_245_4d/2 +GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_88_257_50/2 +GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_9_179_52/2 +CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_250_57/2 +AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_272_5a/2 +TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_114_277_5b/2 +TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_279_5f/2 +AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_293_60/2 +CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_297_61/2 +CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_295_63/2 +TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII