ngs_VERSE

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.