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