def count_chunks(infiles, outfile):
gtffile = infiles[1]
bamfile = infiles[0]
PipelineRnaseq.runFeatureCounts(gtffile,
bamfile,
outfile,
job_threads=2,
strand=0,
options=' -f -O -T 2 --primary -p -B -C')
def count_chunks(infiles, outfile):
gtffile = infiles[1]
bamfile = infiles[0]
PipelineRnaseq.runFeatureCounts(
gtffile,
bamfile,
outfile,
job_threads=PARAMS["featurecounts_threads"],
strand=PARAMS["stranded"],
options="-f " + PARAMS["featurecounts_options"])
def buildFeatureCounts(infiles, outfile):
'''counts reads falling into "features", which by default are genes.
A read overlaps if at least one bp overlaps.
Pairs and strandedness can be used to resolve reads falling into
more than one feature. Reads that cannot be resolved to a single
feature are ignored.
'''
bamfile, annotations = infiles
PipelineRnaseq.runFeatureCounts(annotations,
bamfile,
outfile,
nthreads=PARAMS['featurecounts_threads'],
strand=PARAMS['featurecounts_strand'],
options=PARAMS['featurecounts_options'])
def buildFeatureCounts(infiles, outfile):
'''counts reads falling into "features", which by default are genes.
A read overlaps if at least one bp overlaps.
Pairs and strandedness can be used to resolve reads falling into
more than one feature. Reads that cannot be resolved to a single
feature are ignored.
'''
bamfile, annotations = infiles
PipelineRnaseq.runFeatureCounts(
annotations,
bamfile,
outfile,
nthreads=PARAMS['featurecounts_threads'],
strand=PARAMS['featurecounts_strand'],
options=PARAMS['featurecounts_options'])
