yanmc / chipexo

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.