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

bdgpeakcall 2.0.9.1                                April 2013                                     BDGPEAKCALL(1)