bdgpeakcall(1) Naive call peaks from a single bedGraph track for scores


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


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


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