NAME

       bdgbroadcall - Fine-tuning script to call broad peaks from a single bedGraph track for scores

SYNOPSIS

       bdgbroadcall <-i bedGraph> [-c CUTOFF1] [-C CUTOFF2] [-l MIN] [-g MAX1] [-G MAX2] [-o PREFIX]

DESCRIPTION

       Call  broad  peaks from MACS pvalue or qscore score bedGraph output, with customized settings. Output two
       files for narrow peaks in encodePeak format, and one for broad peaks in bed12 format.

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 CUTOFFPEAK, --cutoff-peak=CUTOFFPEAK
              Cutoff for peaks depending on which method you used for score track. If the file  contains  qvalue
              scores from MACS2, score 2 means qvalue 0.01. DEFAULT: 2

       -C CUTOFFLINK, --cutoff-link=CUTOFFLINK
              Cutoff  for  linking  regions/low  abundance  regions depending on which method you used for score
              track. If the file contains qvalue scores from MACS2, score 1 means  qvalue  0.1,  and  score  0.3
              means qvalue 0.5.  DEFAULT: 5

       -l MINLEN, --min-length=MINLEN
              minimum length of peak, better to set it as d value.  DEFAULT: 200

       -g LVL1MAXGAP, --lvl1-max-gap=LVL1MAXGAP
              maximum gap between significant peaks, better to set it as tag size. DEFAULT: 30

       -G LVL2MAXGAP, --lvl2-max-gap=LVL2MAXGAP
              maximum linking between significant peaks, better to set it as 4 times of d value. DEFAULT: 800

       -o OPREFIX, --o-prefix=OPREFIX
              output file prefix, DEFAULT: peak

bdgbroadcall 2.0.9.1                               April 2013                                    BDGBROADCALL(1)