Penn SCAP-T Pipeline: Documentation
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Module: VERSE
This module will run Verse on the uniquely aligned output from either RUM or STAR (STAR by default).
Usage: ngs.sh verse [-i inputDir] [-f inputFile] [-stranded] [-l features] [-lines_sines] [-id idAttr] -p numProc -s species sampleID Input: sampleID/inputDir/inputFile Output: sampleID/verse/sampleID.verse.cnts.txt sampleID/verse/sampleID.verse.log.txt sampleID/verse/sampleID.verse.err.txt Requires: VERSE version 0.1.1 or later ( http://kim.bio.upenn.edu/software/verse.shtml ). Options: -i inputDir - location of source file (default: star). -f inputFile - source file (default: sampleID.star.unique.bam). -stranded - use strand information (default: no). -p numProc - maximum number of cpu to use. -l features - ordered, comma or semicolon separated list of feature types for verse hierarchical assignment. (default: exon) -lines_sines - also compute line and sine counts, using intersection-nonempty (default: no) This count will be independant of counts for exons/introns/intergenic regions. The output file will have the suffix 'xine'. -id idAttr - name of the the GTF field that contains the name/ID of a gene (default: gene_id). Counts will sum all features with the same value for this field. -s species - species from repository: /lab/repo/resources/verse.
Run VERSE gene quantification. This requires a BAM file as generated by either RUMALIGN or STAR (STAR by default). The following VERSE parameter values are used for exon counting: -z 3 (intersection_nonempty) Each type of feature being counted (i.e. exons, introns, intergentic, lines and sines) will be run in sucession, and generate separate counts files, in the form: SampleID.verse.exon.cnts.txt: exon counts SampleID.verse.intron.cnts.txt: intron counts For a description of the VERSE parameters see the documentation.