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