| Previous changeset 19:42ce70172b72 (2024-02-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 |
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modified:
macros.xml rg_rnaStarSolo.xml test-data/rnastar_test.log |
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added:
test-data/filtered3.vcf test-data/filtered4.bam test-data/rnastar_test_splicejunctions_wasp.bed |
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| diff -r 42ce70172b72 -r 45795f582ae9 macros.xml --- a/macros.xml Wed Feb 14 09:04:09 2024 +0000 +++ b/macros.xml Tue Aug 27 14:11:53 2024 +0000 |
| [ |
| b'@@ -5,7 +5,7 @@\n the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->\n <!-- STAR version to be used -->\n <token name="@TOOL_VERSION@">2.7.11a</token>\n- <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n <token name="@PROFILE@">21.01</token>\n <!-- STAR index version compatible with this version of STAR\n This is the STAR version that introduced the index structure expected\n@@ -17,16 +17,14 @@\n <token name="@IDX_VERSION@">2.7.4a</token>\n <token name="@IDX_VERSION_SUFFIX@">2</token>\n <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>\n-\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">star</requirement>\n <requirement type="package" version="1.18">samtools</requirement>\n <requirement type="package" version="1.13">gzip</requirement>\n- <yield />\n+ <yield/>\n </requirements>\n </xml>\n-\n <xml name="edam">\n <edam_topics>\n <edam_topic>topic_3170</edam_topic>\n@@ -36,20 +34,16 @@\n <edam_operation>operation_0292</edam_operation>\n </edam_operations>\n </xml>\n-\n <xml name="index_selection" token_with_gene_model="0">\n- <param argument="--genomeDir" type="select"\n- label="Select reference genome"\n- help="If your genome of interest is not listed, contact the Galaxy team">\n+ <param argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">\n <options from_data_table="@IDX_DATA_TABLE@">\n- <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />\n- <filter type="static_value" column="5" value="@IDX_VERSION@" />\n- <filter type="sort_by" column="2" />\n- <validator type="no_options" message="No indexes are available for the selected input dataset" />\n+ <filter type="static_value" column="4" value="@WITH_GENE_MODEL@"/>\n+ <filter type="static_value" column="5" value="@IDX_VERSION@"/>\n+ <filter type="sort_by" column="2"/>\n+ <validator type="no_options" message="No indexes are available for the selected input dataset"/>\n </options>\n </param>\n </xml>\n-\n <token name="@FASTQ_GZ_OPTION@">\n --readFilesCommand zcat\n </token>\n@@ -59,9 +53,9 @@\n </citations>\n </xml>\n <xml name="SJDBOPTIONS">\n- <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"/>\n- <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: \'exon\', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as \'gene\', \'transcript\', \'CDS\'."/>\n- <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"/>\n+ <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"/>\n+ <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: \'exon\', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as \'gene\', \'transcript\', \'CDS\'."/>\n+ <param argument="--sjdbOverhang" type="inte'..b' <option value="-">No per gene or transcript output as no GTF was provided</option>\n </param>\n- <when value="-" />\n+ <when value="-"/>\n </conditional>\n </xml>\n <xml name="outSAMmapqUnique">\n <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value\n - according to SAM/BAM specs it means "undefined".\n - 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. -->\n- <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"\n- label="MAPQ value for unique mappers"\n- 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\n-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." />\n+ <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 Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2."/>\n+ </xml>\n+ <xml name="wasp">\n+ <!--\n+ This is re-implementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker,\n+ Yoav Gilad and Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12,\n+ 1061\xe2\x80\x931063 (2015) https://www.nature.com/articles/nmeth.3582. WASP filtering is activated\n+ with "waspOutputMode SAMtag".\n+ -->\n+ <conditional name="wasp_conditional">\n+ <param argument="--waspOutputMode" type="select" label="Actiavte WASP filtering">\n+ <help><![CDATA[This is a reimplementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker,\n+ Yoav Gilad and Jonathan K Pritchard. https://doi.org/10.1038/nmeth.3582. This option will add the vW tag to the SAM output. vW:i:1 means\n+ alignment passed WASP filtering, and all other values mean it did not:<br/>\n+ - vW:i:2 = multi-mapping read<br/>\n+ - vW:i:3 = variant base in the read is N (non-ACGT)<br/>\n+ - vW:i:4 = remapped read did not map <br/>\n+ - vW:i:5 = remapped read multi-maps <br/>\n+ - vW:i:6 = remapped read maps to a different locus <br/>\n+ - vW:i:7 = read overlaps too many variants <br/>\n+ ]]>\n+ </help>\n+ <option value="" selected="true">No WASP filtering</option>\n+ <option value="wasp_mode">Activate WASP filtering</option>\n+ </param>\n+ <when value="wasp_mode">\n+ <param argument="--varVCFfile" type="data" format="vcf" label="VCF file with personal variants" help="Each variant is expected to have a genotype with two alleles. The VCF file needs to have the 10th column with genotype recorded as 0/1, 1/0, 1/1 (or | instead of /)"/>\n+ </when>\n+ <when value=""/>\n+ </conditional>\n </xml>\n </macros>\n' |
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| diff -r 42ce70172b72 -r 45795f582ae9 rg_rnaStarSolo.xml --- a/rg_rnaStarSolo.xml Wed Feb 14 09:04:09 2024 +0000 +++ b/rg_rnaStarSolo.xml Tue Aug 27 14:11:53 2024 +0000 |
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| @@ -94,6 +94,11 @@ --soloCBwhitelist None #end if + #if $solo.wasp_conditional.waspOutputMode == "wasp_mode": + --waspOutputMode SAMtag + --varVCFfile '$solo.wasp_conditional.varVCFfile' + #end if + --soloStrand $solo.soloStrand --soloFeatures $solo.soloFeatures --soloUMIdedup $sc.umidedup.soloUMIdedup @@ -355,6 +360,7 @@ <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> <option value="Gene Velocyto">Velocyto: calculate spliced, unspliced, and ambiguous counts per cell per gene similar to the velocyto tool</option> </param> + <expand macro="wasp"/> <conditional name="filter" > <param name="filter_type" type="select" label="Cell filtering type and parameters" > <option value="cellranger2" selected="true" >Simple filtering of CellRanger v2</option> @@ -515,6 +521,10 @@ <param name="soloStrand" value="Forward" /> <param name="soloFeatures" value="Gene" /> <param name="quantModeGene" value="true" /> + <conditional name="wasp_conditional"> + <param name="waspOutputMode" value="wasp_mode"/> + <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" /> + </conditional> </section> <output name="output_barcodes" > <assert_contents> @@ -544,7 +554,7 @@ <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="output_BAM" value="filtered4.bam" ftype="bam" lines_diff="6"/> <output name="reads_per_gene" > <assert_contents> <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" /> |
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| diff -r 42ce70172b72 -r 45795f582ae9 test-data/filtered3.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered3.vcf Tue Aug 27 14:11:53 2024 +0000 |
| b |
| b'@@ -0,0 +1,175 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##bcftoolsVersion=1.15.1+htslib-1.15.1\n+##bcftoolsCommand=mpileup -f filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa filtered3.bam\n+##reference=file://filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa\n+##contig=<ID=21,length=697740>\n+##ALT=<ID=*,Description="Represents allele(s) other than observed.">\n+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">\n+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n+##INFO=<ID=RPBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Read Position Bias (closer to 0 is better)">\n+##INFO=<ID=MQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality Bias (closer to 0 is better)">\n+##INFO=<ID=BQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Base Quality Bias (closer to 0 is better)">\n+##INFO=<ID=MQSBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality vs Strand Bias (closer to 0 is better)">\n+##INFO=<ID=SCBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Soft-Clip Length Bias (closer to 0 is better)">\n+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher\'s exact test to detect strand bias">\n+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">\n+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">\n+##bcftools_callVersion=1.15.1+htslib-1.15.1\n+##bcftools_callCommand=call -mv -Ob -o filtered3.bcf; Date=Tue Aug 27 14:09:53 2024\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tfiltered3.bam\n+21\t13871\t.\tG\tA\t8.19139\t.\tDP=16;VDB=0.163924;SGB=-0.651104;RPBZ=-1.26304;MQBZ=1.7272;BQBZ=1;SCBZ=-0.447396;FS=0;MQ0F=0.0625;AC=1;AN=2;DP4=8,0,8,0;MQ=9\tGT:PL\t0/1:38,0,6\n+21\t13918\t.\tA\tG\t8.05611\t.\tDP=9;VDB=0.12166;SGB=-0.616816;RPBZ=1.03713;MQBZ=-0.154303;BQBZ=0;SCBZ=0.707107;FS=0;MQ0F=0.111111;AC=1;AN=2;DP4=3,0,6,0;MQ=14\tGT:PL\t0/1:40,0,15\n+21\t13924\t.\tG\tA\t27.0767\t.\tDP=11;VDB=0.0108096;SGB=-0.651104;RPBZ=-0.261911;MQBZ=0.968246;BQBZ=-0.745356;SCBZ=-0.931695;FS=0;MQ0F=0.0909091;AC=2;AN=2;DP4=2,0,8,0;MQ=14\tGT:PL\t1/1:54,3,0\n+21\t13928\t.\tG\tC\t34.42\t.\tDP=11;VDB=0.0257451;SGB=-0.670168;FS=0;MQ0F=0.0909091;AC=2;AN=2;DP4=0,0,10,0;MQ=14\tGT:PL\t1/1:64,24,0\n+21\t13962\t.\tA\tG\t3.21856\t.\tDP=13;VDB=0.00595258;SGB=-0.616816;RPBZ=2.14581;MQBZ=0.245201;BQBZ=-0.113961;SCBZ=-1.73888;FS=0;MQ0F=0.0769231;AC=1;AN=2;DP4=7,0,6,0;MQ=12\tGT:PL\t0/1:33,0,34\n+21\t15349\t.\tG\tC\t3.74242\t.\tDP=33;VDB=3.28209e-07;SGB=-0.689466;RPBZ=-1.0584;MQBZ=1.31911;MQSBZ=-1.01601;BQBZ=-1.40181;SCBZ=0.601646;FS=0;MQ0F=0.0606061;AC=1;AN=2;DP4=1,15,1,15;MQ=13\tGT:PL\t0/1:34,0,49\n+21\t15425\t.\tT\tC\t15.3182\t.\tDP=21;VDB=0.739317;SGB=-0.686358;RPBZ=-1.79168;MQBZ=0.125524;BQBZ=1.41022;SCBZ=0.514874;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,7,0,14;MQ=12\tGT:PL\t0/1:47,0,9\n+21\t15431\t.\tG\tA\t6.81655\t.\tDP=18;VDB=0.777008;SGB=-0.683931;RPBZ=-0.93741;MQBZ=-1.01859;BQBZ=1.61245;SCBZ=-1.53815;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,5,0,13;MQ=10\tGT:PL\t0/1:38,0,11\n+21\t19605\t.\tA\t'..b';FS=0;MQ0F=0;AC=2;AN=2;DP4=4,0,5,0;MQ=11\tGT:PL\t1/1:37,3,0\n+21\t152547\t.\tA\tG\t8.54666\t.\tDP=8;VDB=0.00477428;SGB=-0.636426;RPBZ=0.223607;MQBZ=-0.774597;BQBZ=-0.377964;SCBZ=0.377964;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,7,0;MQ=12\tGT:PL\t1/1:35,4,0\n+21\t221789\t.\tT\tC\t19.4636\t.\tDP=5;VDB=0.300397;SGB=-0.590765;FS=0;MQ0F=0.2;AC=2;AN=2;DP4=0,0,5,0;MQ=12\tGT:PL\t1/1:49,15,0\n+21\t221824\t.\tA\tG\t17.2912\t.\tDP=5;VDB=0.446842;SGB=-0.556411;RPBZ=0;MQBZ=0.790569;BQBZ=0;SCBZ=0;FS=0;MQ0F=0.2;AC=2;AN=2;DP4=1,0,4,0;MQ=12\tGT:PL\t1/1:44,8,0\n+21\t236291\t.\tA\tG\t3.21958\t.\tDP=7;VDB=0.535497;SGB=-0.556411;RPBZ=0.707107;MQBZ=-0.866025;BQBZ=0;SCBZ=-0.585142;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,3,0,4;MQ=17\tGT:PL\t0/1:33,0,31\n+21\t236294\t.\tC\tT\t4.32521\t.\tDP=6;VDB=0.176409;SGB=-0.556411;RPBZ=1.38873;MQBZ=-0.707107;BQBZ=0;SCBZ=0.491869;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,2,0,4;MQ=16\tGT:PL\t0/1:35,0,19\n+21\t236295\t.\tA\tG\t4.32521\t.\tDP=6;VDB=0.522837;SGB=-0.556411;RPBZ=0;MQBZ=-0.707107;BQBZ=0;SCBZ=-1.47561;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,2,0,4;MQ=16\tGT:PL\t0/1:35,0,19\n+21\t236320\t.\tG\tA\t3.20067\t.\tDP=8;VDB=0.220638;SGB=-0.556411;RPBZ=1.76777;MQBZ=0;BQBZ=-0.866025;SCBZ=0.866025;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,3,0,4;MQ=14\tGT:PL\t0/1:33,0,20\n+21\t236327\t.\tA\tG\t6.77159\t.\tDP=6;VDB=0.673544;SGB=-0.590765;RPBZ=-0.29277;MQBZ=-0.69282;BQBZ=-0.447214;SCBZ=0.69282;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,5;MQ=14\tGT:PL\t1/1:34,0,2\n+21\t236359\t.\tA\tT\t8.99921\t.\tDP=4;VDB=0.160409;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,4;MQ=11\tGT:PL\t1/1:38,12,0\n+21\t248947\t.\tT\tC\t4.85359\t.\tDP=4;VDB=0.38;SGB=-0.453602;RPBZ=-0.774597;MQBZ=1.73205;MQSBZ=-1;BQBZ=0;SCBZ=1;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,2,1,1;MQ=11\tGT:PL\t1/1:30,2,0\n+21\t248966\t.\tG\tA\t12.6566\t.\tDP=4;VDB=0.112085;SGB=-0.556411;MQSBZ=-1;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,1,3;MQ=11\tGT:PL\t1/1:42,12,0\n+21\t251560\t.\tC\tT\t11.7172\t.\tDP=3;VDB=0.137328;SGB=-0.511536;MQSBZ=0.707107;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=14\tGT:PL\t1/1:41,9,0\n+21\t289446\t.\tT\tC\t49.4146\t.\tDP=22;VDB=1.4824e-07;SGB=-0.692562;FS=0;MQ0F=0.0454545;AC=2;AN=2;DP4=0,0,22,0;MQ=12\tGT:PL\t1/1:79,66,0\n+21\t289481\t.\tT\tC\t3.73429\t.\tDP=48;VDB=0.22406;SGB=-0.692976;RPBZ=0.341551;MQBZ=-1.11595;BQBZ=-1.2128;SCBZ=-1.70538;FS=0;MQ0F=0.0208333;AC=1;AN=2;DP4=22,0,26,0;MQ=11\tGT:PL\t0/1:34,0,44\n+21\t289488\t.\tT\tC\t6.50824\t.\tDP=50;VDB=0.518994;SGB=-0.693021;RPBZ=0.545171;MQBZ=-1.485;BQBZ=2.489;SCBZ=-1.74235;FS=0;MQ0F=0.04;AC=1;AN=2;DP4=23,0,27,0;MQ=11\tGT:PL\t0/1:38,0,40\n+21\t289520\t.\tA\tC\t21.7432\t.\tDP=41;VDB=4.57336e-05;SGB=-0.69312;RPBZ=-0.393988;MQBZ=0.311388;BQBZ=2.69313;SCBZ=1.10119;FS=0;MQ0F=0.0243902;AC=2;AN=2;DP4=9,0,32,0;MQ=10\tGT:PL\t1/1:49,21,0\n+21\t289647\t.\tG\tA\t3.22451\t.\tDP=3;VDB=0.873285;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=14\tGT:PL\t1/1:30,9,0\n+21\t339923\t.\tC\tT\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t355659\t.\tC\tT\t6.32811\t.\tDP=4;VDB=0.868052;SGB=-0.511536;RPBZ=-1.34164;MQBZ=1;BQBZ=0;SCBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,3;MQ=11\tGT:PL\t1/1:32,5,0\n+21\t553515\t.\tC\tG\t7.30814\t.\tDP=2;VDB=0.68;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t602273\t.\tA\tC\t6.32811\t.\tDP=4;VDB=0.131948;SGB=-0.511536;RPBZ=-1.34164;MQBZ=1;BQBZ=-0.57735;SCBZ=-1.73205;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,3;MQ=11\tGT:PL\t1/1:32,5,0\n+21\t682407\t.\tG\tT\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t682421\t.\tT\tG\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t682423\t.\tC\tG\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t682426\t.\tG\tA\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t682568\t.\tA\tG\t8.13869\t.\tDP=5;VDB=0.133161;SGB=-0.590765;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,5;MQ=9\tGT:PL\t1/1:37,15,0\n+21\t694476\t.\tC\tG\t18.4764\t.\tDP=6;VDB=0.0341101;SGB=-0.616816;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,6,0;MQ=11\tGT:PL\t1/1:48,18,0\n+21\t694482\t.\tT\tC\t19.4636\t.\tDP=4;VDB=0.131345;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,4,0;MQ=15\tGT:PL\t1/1:49,12,0\n' |
| b |
| diff -r 42ce70172b72 -r 45795f582ae9 test-data/filtered4.bam |
| b |
| Binary file test-data/filtered4.bam has changed |
| b |
| diff -r 42ce70172b72 -r 45795f582ae9 test-data/rnastar_test.log --- a/test-data/rnastar_test.log Wed Feb 14 09:04:09 2024 +0000 +++ b/test-data/rnastar_test.log Tue Aug 27 14:11:53 2024 +0000 |
| b |
| @@ -3,32 +3,35 @@ Finished on | .* Mapping speed, Million of reads per hour | .* - Number of input reads | 100 - Average input read length | 75 + Number of input reads | 15447 + Average input read length | 119 UNIQUE READS: - Uniquely mapped reads number | 99 - Uniquely mapped reads % | 99.00% - Average mapped length | 74.65 - Number of splices: Total | 52 + Uniquely mapped reads number | 150 + Uniquely mapped reads % | 0.97% + Average mapped length | 105.11 + Number of splices: Total | 131 Number of splices: Annotated (sjdb) | 0 - Number of splices: GT/AG | 52 - Number of splices: GC/AG | 0 - Number of splices: AT/AC | 0 - Number of splices: Non-canonical | 0 - Mismatch rate per base, % | 2.00% - Deletion rate per base | 0.00% - Deletion average length | 0.00 - Insertion rate per base | 0.00% - Insertion average length | 0.00 + Number of splices: GT/AG | 100 + Number of splices: GC/AG | 6 + Number of splices: AT/AC | 1 + Number of splices: Non-canonical | 24 + Mismatch rate per base, % | 6.68% + Deletion rate per base | 0.04% + Deletion average length | 1.17 + Insertion rate per base | 0.04% + Insertion average length | 1.50 MULTI-MAPPING READS: - Number of reads mapped to multiple loci | 1 - % of reads mapped to multiple loci | 1.00% - Number of reads mapped to too many loci | 0 - % of reads mapped to too many loci | 0.00% + Number of reads mapped to multiple loci | 451 + % of reads mapped to multiple loci | 2.92% + Number of reads mapped to too many loci | 58 + % of reads mapped to too many loci | 0.38% UNMAPPED READS: + Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% - % of reads unmapped: too short | 0.00% - % of reads unmapped: other | 0.00% + Number of reads unmapped: too short | 7912 + % of reads unmapped: too short | 51.22% + Number of reads unmapped: other | 6876 + % of reads unmapped: other | 44.51% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% |
| b |
| diff -r 42ce70172b72 -r 45795f582ae9 test-data/rnastar_test_splicejunctions_wasp.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_splicejunctions_wasp.bed Tue Aug 27 14:11:53 2024 +0000 |
| b |
| @@ -0,0 +1,193 @@ +21 13873 52149 1 1 0 0 1 12 +21 13882 20712 2 2 0 0 3 28 +21 13882 29808 2 2 0 0 1 28 +21 13882 35980 2 2 0 0 1 26 +21 13882 50180 2 2 0 0 1 19 +21 13887 27728 1 1 0 0 1 21 +21 13887 35985 1 1 0 0 1 15 +21 13887 51866 1 1 0 0 4 40 +21 13887 62408 1 1 0 0 2 24 +21 13887 88031 1 1 0 0 2 40 +21 13887 152470 1 1 0 2 2 40 +21 13894 50193 1 1 0 0 1 24 +21 13907 27883 2 2 0 0 2 45 +21 13976 19932 2 2 0 0 4 41 +21 13976 88119 2 2 0 0 2 33 +21 13976 108267 2 2 0 0 2 33 +21 13991 30873 2 2 0 0 1 18 +21 13991 52131 2 2 0 0 1 18 +21 15394 46773 1 1 0 0 1 39 +21 18885 50205 2 4 0 0 1 35 +21 18949 28120 1 1 0 0 1 26 +21 18953 27816 2 2 0 0 1 16 +21 18953 37719 2 2 0 1 0 34 +21 19001 46120 2 2 0 0 1 17 +21 19001 52299 2 2 0 0 1 17 +21 19001 63039 2 2 0 0 1 17 +21 19533 60698 2 2 0 1 0 44 +21 19658 51267 1 1 0 0 1 45 +21 19737 28120 1 1 0 0 1 16 +21 19826 51848 1 1 0 1 1 36 +21 19830 37617 1 1 0 0 2 12 +21 19842 20715 1 1 0 0 1 23 +21 19842 51866 1 1 0 1 0 22 +21 19842 62903 1 1 0 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1 0 0 1 38 +21 46057 62479 1 1 0 0 1 14 +21 46065 143522 1 1 0 0 2 45 +21 46069 88115 1 1 0 1 2 41 +21 46073 88119 2 2 0 0 1 29 +21 46814 70282 2 2 0 0 1 32 +21 46870 51210 2 2 0 1 0 21 +21 50168 62885 1 1 0 0 1 18 +21 50168 81335 1 1 0 0 1 34 +21 50244 137072 2 2 0 0 2 35 +21 50274 88119 2 2 0 0 1 39 +21 50274 91677 2 2 0 0 1 13 +21 50658 51848 1 1 0 1 0 42 +21 51216 75722 2 2 0 0 2 21 +21 51280 56626 2 2 0 0 1 19 +21 51288 75795 2 2 0 0 1 22 +21 51288 149429 2 2 0 0 2 41 +21 51293 60852 1 1 0 1 1 29 +21 51293 117556 1 1 0 0 2 44 +21 51302 60411 2 2 0 0 1 33 +21 51302 60861 2 2 0 0 2 42 +21 51320 75826 1 1 0 0 1 34 +21 51849 62390 1 1 0 0 1 37 +21 51849 62885 1 1 0 1 0 18 +21 51853 52149 1 1 0 0 1 12 +21 51899 52192 1 1 0 0 1 22 +21 51899 120538 1 1 0 1 4 32 +21 51955 206521 2 2 0 1 2 27 +21 52117 62856 2 2 0 0 3 18 +21 52162 62903 1 1 0 1 0 14 +21 52162 81353 1 1 0 0 1 44 +21 52162 88031 1 1 0 1 5 44 +21 52162 98665 1 1 0 0 1 36 +21 52162 152470 1 1 0 0 3 44 +21 52162 289491 1 1 0 1 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33 +21 81438 88115 1 1 0 0 1 36 +21 88064 120538 1 1 0 1 5 32 +21 88120 91677 2 2 0 0 1 26 +21 91565 115886 1 1 0 0 2 33 +21 91597 120538 1 1 0 0 1 25 +21 98666 143455 1 1 0 1 0 18 +21 98750 138516 1 1 0 0 1 14 +21 108179 115881 2 2 0 0 1 38 +21 108223 152509 2 2 0 0 1 25 +21 112412 138384 2 2 0 0 1 16 +21 115887 152470 1 1 0 0 1 22 +21 115919 120538 1 1 0 0 7 43 +21 126053 137131 1 1 0 0 1 26 +21 131927 138384 2 2 0 0 1 21 +21 136828 136968 2 2 0 0 2 26 +21 137014 289491 1 1 0 0 6 25 +21 137087 137268 1 1 0 0 1 14 +21 137346 138586 1 1 0 0 1 19 +21 138427 152465 2 2 0 1 6 40 +21 138432 152470 1 1 0 0 2 31 +21 138513 143522 1 1 0 0 2 45 +21 682607 689282 2 2 0 1 0 36 |