GeneTrack separately identifies peaks on the forward "+â€ (W) and reverse â€œ-â€ (C) strand.
genetrack.py [options] input_paths
-h, --help show this help message and exit
-s SIGMA Sigma to use when smoothing reads to call peaks. Default 5
-e EXCLUSION Exclusion zone around each peak that prevents others from being called. Default 20.
-u UP_WIDTH Upstream width of called peaks. Default uses half exclusion zone.
-d DOWN_WIDTH Downstream width of called peaks. Default uses half exclusion zone.
-F FILTER Absolute read filter; outputs only peaks with larger peak height. Default 3.
-c CHROMOSOME Chromosome (ex chr11) to limit to. Default process all.
-k CHUNK_SIZE Size, in millions of base pairs, to chunk each chromosome into when processing. Each 1 million size uses approximately 20MB of memory. Default 10.
-o FORMAT Output format for called peaks. Valid formats are gff and txt. Default gff.
-b Output bed graph tracks.
-v Verbose mode: displays debug messages.