This is a standalone version of GeneTrack. It was written by a Penn State freshman student Pindi Albert during an internship with the Pugh lab at Penn State.
It implements the peak calling algorithm as described in the paper "GeneTrack--a genomic data processing and visualization framework" published in Bioinformatics 2008, http://www.ncbi.nlm.nih.gov/pubmed/18388141 It does not however implement the visualization interface that was described in the paper.
Usage:
python genetrack/genetrack.py
This will print a help on usage.
The input files should be in BED
, GFF
or the internal .idx
format.
Detailed usage:
Usage: genetrack.py [options] input_paths
input_paths may be:
- a file to run on
- "-" to run on standard input
example usage:
python genetrack.py -s 10 /path/to/a/file.txt
python genetrack.py -s 5 -e 50 -
Options:
-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.