NAME¶

bdgpeakcall - Naive call peaks from a single bedGraph track for scores

SYNOPSIS¶

bdgpeakcall <-i bedGraph> [-c CUTOFF] [-l MIN] [ -g MAX] [-o PREFIX]

DESCRIPTION¶

Call peaks from MACS pvalue or qscore score bedGraph output, with customized settings. Output encodePeak format peaks, combining peak boundaries, peak summits.

OPTIONS¶

--version

show program's version number and exit

-h, --help

Show this help message and exit.

-i IFILE, --ifile=IFILE

MACS pvalue score bedGraph

-c CUTOFF, --cutoff=CUTOFF

Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. DEFAULT: 5

-l MINLEN, --min-length=MINLEN

minimum length of peak, better to set it as d value. DEFAULT: 200

-g MAXGAP, --max-gap=MAXGAP

maximum gap between significant points in a peak, better to set it as tag size. DEFAULT: 30

-o OPREFIX, --o-prefix=OPREFIX

output file prefix, DEFAULT: peak