Mercurial > repos > iuc > rgrnastar
changeset 23:a2b0feda6933 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 16:56:55 2022 +0000 +++ b/macros.xml Fri Feb 17 20:03:27 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_rnaStar.xml Tue Nov 01 16:56:55 2022 +0000 +++ b/rg_rnaStar.xml Fri Feb 17 20:03:27 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy1" profile="20.01" license="MIT"> +<tool id="rna_star" name="RNA STAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> <description>Gapped-read mapper for RNA-seq data</description> <macros> <import>macros.xml</import> @@ -65,9 +65,9 @@ #end if #end if - --quantMode ${quantmode_output.quantMode} - #if 'TranscriptomeSAM' in str($quantmode_output.quantMode): - --quantTranscriptomeBan ${quantmode_output.quantTranscriptomeBan} + --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode} + #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode): + --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan} #end if ## Output format parameters @@ -206,9 +206,7 @@ #end if ## Limits - --limitOutSJoneRead $algo.params.limits.limitOutSJoneRead - --limitOutSJcollapsed $algo.params.limits.limitOutSJcollapsed - --limitSjdbInsertNsj $algo.params.limits.limitSjdbInsertNsj + @LIMITS@ #else: ## Go with STAR's default algorithmic settings, ## but we need to provide a reasonable default @@ -238,14 +236,19 @@ --chimOutJunctionFormat 1 #end if #end if + + ##outWig: + @OUTWIG@ && ## recompress BAM output for smaller file size samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam - #if 'TranscriptomeSAM' in str($quantmode_output.quantMode): + #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode): ## same recompression for optional transcriptome BM && samtools view -b -o '$transcriptome_mapped_reads' Aligned.toTranscriptome.out.bam #end if + ##outWig: + @OUTWIGOUTPUTS@ ]]></command> <inputs> @@ -279,15 +282,22 @@ <param name="GTFselect" type="select" label="Reference genome with or without an annotation" help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and, optionally, provide your own splice-junction annonations."> - <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option> + <option value="without-gtf-with-gtf" selected='true'>use genome reference without builtin gene-model but provide a gtf</option> + <option value="without-gtf">use genome reference without builtin gene-model and do not provide a gtf</option> <option value="with-gtf">use genome reference with builtin gene-model</option> </param> <when value="with-gtf"> <expand macro="index_selection" with_gene_model="1" /> + <expand macro="quantMode" /> + </when> + <when value="without-gtf-with-gtf"> + <expand macro="index_selection" with_gene_model="0" /> + <expand macro="SJDBOPTIONS"/> + <expand macro="quantMode" /> </when> <when value="without-gtf"> <expand macro="index_selection" with_gene_model="0" /> - <expand macro="@SJDBOPTIONS@" /> + <expand macro="quantModeNoGTF" /> </when> </conditional> </when> @@ -301,9 +311,12 @@ <option value="with-gtf">build index with gene-model</option> </param> <when value="with-gtf"> - <expand macro="@SJDBOPTIONS@" optional="false"/> + <expand macro="SJDBOPTIONS"/> + <expand macro="quantMode" /> </when> - <when value="without-gtf" /> + <when value="without-gtf"> + <expand macro="quantModeNoGTF" /> + </when> </conditional> </when> </conditional> @@ -335,28 +348,6 @@ label="Pregenerated splice junctions datasets of your samples" /> </when> </conditional> - <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> <param argument="--chimOutType" type="select" label="Report chimeric alignments?" help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored."> @@ -365,7 +356,6 @@ <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option> <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option> <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option> - <option value="WithinBAM Junctions">Deprecated: In both forms (WithinBAM Junctions)</option> </param> <section name="oformat" title="BAM output format specification" expanded="true"> @@ -373,17 +363,10 @@ label="Read alignment tags to include in the BAM output" help="Note on using the XS tag: If the XS tag is used, STAR will filter out alignments with undefined strand (i.e., those containing only non-canonical unannotated junctions). Using this tag is recommended if you plan to use the STAR results with STAR-Fusion. In addition, it is required for compatibility with Cufflinks if your sequences come from an unstranded library preparation."> - <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> + <expand macro="common_SAM_attributes"/> + <option value="MC">MC (CIGAR string for mate/next segment)</option> <option value="XS">XS (strand flag, see parameter help below) </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="MC">MC (CIGAR string for mate/next segment)</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> - <option value="ch" selected="true">ch (used to indicate chimeric alignments)</option> + <option value="ch" selected="true">ch (used to indicate chimeric alignments)</option> <!--This is not the default in STAR--> </param> <param argument="--outSAMattrIHstart" name="HI_offset" type="select" display="radio" label="HI tag values should be"> @@ -403,10 +386,13 @@ label="Would you like all alignments with the best score labeled primary?"/> --> <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" /> - <param argument="--outSAMmapqUnique" type="integer" value="60" min="30" max="255" + <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value + - according to SAM/BAM specs it means "undefined". + - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. --> + <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255" label="MAPQ value for unique mappers" help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is -used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflinks." /> +used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." /> </section> <section name="filter" title="Output filter criteria" expanded="true"> <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true" @@ -469,7 +455,7 @@ </section> <section name="align" title="Alignment parameters" expanded="false"> - <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/> + <param argument="--alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/> <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/> <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/> <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/> @@ -485,7 +471,12 @@ <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/> <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/> <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/> - <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/> + <param argument="--alignEndsType" type="select" label="type of read ends alignment"> + <option value="Local">standard local alignment with soft-clipping allowed</option> + <option value="EndToEnd">force end-to-end read alignment, do not soft-clip</option> + <option value="Extend5pOfRead1">fully extend only the 5p of the read1, all other ends: local alignment</option> + <option value="Extend5pOfReads12">fully extend only the 5p of the both read1 and read2, all other ends: local alignment</option> + </param> <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0" label="minimum number of overlap bases to trigger mates merging and realignment" /> <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01" @@ -519,11 +510,7 @@ label="Score range for multi-mapping chimeras" help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" /> </section> - <section name="limits" title="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> + <expand macro="limits" /> </when> </conditional> </section> @@ -531,6 +518,7 @@ <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50. Tweak this if you are facing memory-related errors." /> <param argument="--winAnchorMultimapNmax" type="integer" value="50" min="50" label="Maximum number of loci anchors are allowed to map to" help="Higher value can increase the runtime singificantly. This value should be set greater or equal to --outFilterMultimapNmax" /> </section> + <expand macro="outWig"/> </inputs> <outputs> @@ -552,14 +540,16 @@ </data> <data name="transcriptome_mapped_reads" format="unsorted.bam" label="${tool.name} on ${on_string}: transcriptome-mapped.bam" > - <filter>'TranscriptomeSAM' in quantmode_output['quantMode']</filter> + <filter>'TranscriptomeSAM' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter> <expand macro="dbKeyActions" /> </data> <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab"> - <filter>'GeneCounts' in quantmode_output['quantMode']</filter> + <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter> <expand macro="dbKeyActions" /> + <expand macro="outCountActions" /> </data> + <expand macro="outWigOutputs"/> </outputs> <tests> @@ -570,12 +560,11 @@ </conditional> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> - <param name="genomeFastaFiles" value="tophat_test.fa" /> + <param name="genomeFastaFiles" value="tophat_test.fa.gz" /> <param name="genomeSAindexNbases" value="5" /> </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="algo"> <conditional name="params"> @@ -601,7 +590,6 @@ </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="algo"> <conditional name="params"> @@ -626,14 +614,13 @@ <param name="GTFselect" value="with-gtf" /> <param name="sjdbOverhang" value="75"/> <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> + <conditional name="quantmode_output"> + <param name="quantMode" value="GeneCounts"/> + </conditional> </conditional> </conditional> - <conditional name="quantmode_output"> - <param name="quantMode" value="GeneCounts"/> - </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="algo"> <conditional name="params"> @@ -660,14 +647,13 @@ <param name="GTFselect" value="with-gtf" /> <param name="sjdbOverhang" value="75"/> <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> + <conditional name="quantmode_output"> + <param name="quantMode" value="TranscriptomeSAM"/> + </conditional> </conditional> </conditional> - <conditional name="quantmode_output"> - <param name="quantMode" value="TranscriptomeSAM"/> - </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="algo"> <conditional name="params"> @@ -680,6 +666,39 @@ <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" /> </test> + <!-- test cached no index but gtf file and GeneCounts TranscriptomeSAM mode --> + <test expect_num_outputs="5"> + <conditional name="singlePaired"> + <param name="sPaired" value="single" /> + <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> + </conditional> + <conditional name="refGenomeSource"> + <param name="geneSource" value="indexed" /> + <conditional name="GTFconditional"> + <param name="GTFselect" value="without-gtf-with-gtf" /> + <param name="genomeDir" value="000" /> + <param name="sjdbOverhang" value="75"/> + <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> + <conditional name="quantmode_output"> + <param name="quantMode" value="TranscriptomeSAM GeneCounts"/> + </conditional> + </conditional> + </conditional> + <section name="oformat"> + <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> + </section> + <section name="algo"> + <conditional name="params"> + <param name="settingsType" value="default" /> + </conditional> + </section> + + <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> + <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> + <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> + <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" /> + <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" /> + </test> <test expect_num_outputs="3"> <conditional name="singlePaired"> <param name="sPaired" value="single" /> @@ -692,7 +711,6 @@ </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="filter"> <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> @@ -728,7 +746,6 @@ <param name="chimOutType" value="Junctions" /> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="algo"> <conditional name="params"> @@ -751,7 +768,6 @@ <param name="chimOutType" value="Junctions" /> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="algo"> <conditional name="params"> @@ -773,7 +789,6 @@ </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="filter"> <param name="basic_filters" value="--outFilterIntronMotifs RemoveNoncanonical" /> @@ -808,7 +823,6 @@ </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="filter"> <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> @@ -844,7 +858,6 @@ </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="filter"> <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> @@ -880,7 +893,6 @@ </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="filter"> <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> @@ -915,7 +927,6 @@ </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="filter"> <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonicalUnannotated,--outFilterIntronMotifs RemoveNoncanonical" /> @@ -946,7 +957,6 @@ </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="algo"> <conditional name="params"> @@ -969,7 +979,6 @@ </conditional> <section name="oformat"> <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> - <param name="outSAMmapqUnique" value="255" /> </section> <section name="algo"> <conditional name="params"> @@ -980,6 +989,101 @@ <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases_02.bed"/> <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases_02.bam" compare="sim_size" delta="634" /> </test> + <!-- test paired-end input and outWig --> + <test expect_num_outputs="6"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired" /> + <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> + <param name="input2" value="tophat_in3.fastqsanger" ftype="fastqsanger" /> + </conditional> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="tophat_test.fa" /> + <param name="genomeSAindexNbases" value="5" /> + <conditional name="GTFconditional"> + <param name="GTFselect" value="with-gtf" /> + <param name="sjdbOverhang" value="75"/> + <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> + <conditional name="quantmode_output"> + <param name="quantMode" value="GeneCounts"/> + </conditional> + </conditional> + </conditional> + <section name="oformat"> + <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> + </section> + <section name="algo"> + <conditional name="params"> + <param name="settingsType" value="default" /> + </conditional> + </section> + <conditional name="outWig"> + <param name="outWigType" value="wiggle" /> + <param name="outWigTypeSecondWord" value="read2"/> + <param name="outWigStrand" value="false" /> + </conditional> + <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> + <output name="splice_junctions" file="rnastar_test_splicejunctions_PE.bed"/> + <output name="mapped_reads" file="rnastar_test_mapped_reads_PE.bam" compare="sim_size" delta="634" /> + <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE.txt" /> + <output name="signal_unique_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig"/> + <output name="signal_uniquemultiple_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig" /> + </test> + <!-- test paired-end input as collection and outWig stranded --> + <test expect_num_outputs="8"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_collection" /> + <param name="input" > + <collection type="paired"> + <element name="forward" value="tophat_revlib_R1.fastqsanger" ftype="fastq"/> + <element name="reverse" value="tophat_revlib_R2.fastqsanger" ftype="fastq"/> + </collection> + </param> + </conditional> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="tophat_test.fa" /> + <param name="genomeSAindexNbases" value="5" /> + <conditional name="GTFconditional"> + <param name="GTFselect" value="with-gtf" /> + <param name="sjdbOverhang" value="75"/> + <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> + <conditional name="quantmode_output"> + <param name="quantMode" value="GeneCounts"/> + </conditional> + </conditional> + </conditional> + <section name="oformat"> + <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> + </section> + <section name="algo"> + <conditional name="params"> + <param name="settingsType" value="default" /> + </conditional> + </section> + <conditional name="outWig"> + <param name="outWigType" value="bedGraph" /> + </conditional> + + <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> + <output name="splice_junctions"> + <assert_contents> + <has_n_lines n="2"/> + <has_line_matching expression="test_chromosome\s+251\s+350\s+1\s+1\s+0\s+24\s+0\s+33"/> + <has_line_matching expression="test_chromosome\s+401\s+500\s+1\s+1\s+0\s+25\s+0\s+36"/> + </assert_contents> + </output> + <output name="mapped_reads" > + <assert_contents> + <has_size value="4711" delta="800"/> + </assert_contents> + </output> + <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE_rev.txt" /> + <output name="signal_unique_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/> + <output name="signal_uniquemultiple_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/> + <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" /> + <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" /> + </test> </tests> <help><![CDATA[ **What it does** @@ -1024,7 +1128,7 @@ In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity - under *Output filter criteria*, - **Would you like to set additional output filters?**: select `Yes' to set + **Would you like to set additional output filters?**: select `Yes` to set **Maximum number of alignments to output a read's alignment results, plus 1** to 50 - under *Algorithmic settings*, **Configure seed, alignment and limits options**:
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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 20:03:27 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 20:03:27 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 20:03:27 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