{"id":6248,"projects":[69],"description":"Computes a series of quality control metrics for RNA-seq data.\n\nUsage:\n\n-bwa <arg>\nPath to BWA, which should be set if it's not in your path and BWArRNA is used.\n\n-BWArRNA <arg>\nUse an on the fly BWA alignment for estimating rRNA content. The value should be the rRNA reference fasta. If this flag is absent, rRNA estimation will be based upon the rRNA transcript intervals provided in the GTF (a faster but less robust method).\n\n-corr <arg>\nGCT file for expression correlation comparison. Note, that the values must be log normalized, and the identifiers must match those of the GTF file.\n\n-d <arg>\nPerform downsampling to the given number of reads.\n\n-e <arg>\nChange the definition of a transcripts end (5' or 3') to the given length. (50, 100, 200 are acceptable values; 200 is default)\n\n-expr <arg>\nUses provided GCT file for expression values instead of on-the-fly RPKM calculation\n\n-gc <arg>\nFile of transcript id <tab> gc content. Used for stratification.\n\n-n <arg>\nNumber of top transcripts to use. Default is 1000.\n\n-noDoC\nSuppresses GATK Depth of Coverage calculations.\n\n-noReadCounting\nSuppresses read count-based metrics.\n\n-o <arg>\nOutput directory (will be created if doesn't exist).\n\n-r <arg>\nReference Genome in fasta format.\n\n-rRNA <arg>\nintervalFIle for rRNA loci (must end in .list). This is an alternative flag to the -BWArRNA flag.\n\n-s <arg>\nSample File: tab-delimited description of samples and their bams. This file header is:\nSample ID    Bam File    Notes\nWhen running on just one sample, this argument can be a string of the form\n\"Sample ID|Bam File|Notes\", where Bam File is the path to the input file.\n\n-singleEnd\nThis BAM contains single end reads.\n\n-strat <arg>\nStratification options: current supported option is 'gc'\n\n-strictMode <arg>\nWhen counting reads per exon or generating RPKMs, reads will be filtered out that have a mapping quality of zero, more than 6 non-reference bases or improper pairs.\n\n-t <arg>\nGTF File defining transcripts (must end in '.gtf').\n\n-transcriptDetails\nProvide an HTML report for each transcript.\n\n-ttype <arg>\nThe column in GTF to use to look for rRNA transcript type. Mainly used for running on Ensembl GTF (specify \"-ttype 2\"). Otherwise, for spec-conforming GTF files, disregard.\n\n-rRNAdSampleTarget\nDownsamples to calculate rRNA rate more efficiently. Default is 1 million. Set to 0 to disable.\n\n-gcMargin\nUsed in conjunction with '-strat gc' to specify the percent gc content to use as boundaries. E.g. .25 would set a lower cutoff of 25% and an upper cutoff of 75% (default is 0.375).\n\n-gld\nGap Length Distribution: if flag is present, the distribution of gap lengths will be plotted.\n\n-gatkFlags\nPass a string of quotes directly to the GATK (e.g. -gatkFlags \"-DBQ 0\" to set missing base qualities to zero).","image":"","tags":"","type":"","title":"dockstore-tool-rnaseqc","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcancercollaboratory%2Fdockstore-tool-rnaseqc","authors":[1],"rubrics":[25]}