Penn SCAP-T Pipeline: Documentation
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Module: HTSEQ
This module will run HTSeq on the uniquely aligned output from either RUM or STAR (STAR by default).
Usage:
ngs.sh htseq [-i inputDir] [-f inputFile] [-stranded] [-introns] [-id idAttr] -s species sampleID
Input:
sampleID/inputDir/inputFile
Output:
sampleID/htseq/sampleID.htseq.cnts.txt
sampleID/htseq/sampleID.htseq.log.txt
sampleID/htseq/sampleID.htseq.err.txt
Requires:
HTSeq version 0.6 or later ( http://www-huber.embl.de/users/anders/HTSeq/ ). Note that HTSeq requires NumPy.
Pysam ( https://pypi.python.org/pypi/pysam )
dynamicRange.py ( https://github.com/safisher/ngs )
Options:
-i inputDir - location of source file (default: star).
-f inputFile - source file (default: sampleID.star.unique.bam).
-stranded - use strand information (default: no).
-introns - also compute intron counts (default: no). A single GTF file is expected to contain both introns and exon. HTSeq will be run first with type=exon and a second time with type=intron.
-id idAttr - the 'idattr' flag for HTSeq.count() which is the GTF feature that contains the feature ID (default: gene_id).
-s species - species from repository: /lab/repo/resources/htseq.
Run HTSeq using htseq-count script. This requires a BAM file as generated by either RUMALIGN or STAR (STAR by default).
The following HTSeq parameter values are used for exon counting:
--mode=intersection-strict --type=exon
INTRON COUNTING (-introns option):
When intron counting is enabled (-introns) then introns will be counted with intersection-nonempty. In this case three counts files will be generated:
SampleID.htseeq.exons.cnts: exon counts
SampleID.htseeq.introns.cnts: intron counts
SampleID.htseeq.cnts.txt: combined counts tab delimited (gene, exons, introns, total)
For a description of the HTSeq parameters see http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count