NAME

       bdgdiff - Naive call differential peaks from 4 bedGraph tracks for scores

SYNOPSIS

       bdgdiff  <--s1  bedGraph> <--s2 bedGraph> <--s12 bedGraph> <--s21 bedGraph> [-c CUTOFF] [-l MIN] [-g MAX]
       [-o PREFIX]

DESCRIPTION

       Call differential regions from four bedGraph files  of  pair-wise  p/qvalue,  with  customized  settings.
       Please read the descriptions of options carefully.

OPTIONS

       --version
              show program's version number and exit

       -h, --help
              Show this help message and exit.

       --s1=ST1C1BDG
              MACS p/qvalue score bedGraph, condition 1 ChIP treatment against condition 1 control input.

       --s2=ST2C2BDG
              MACS p/qvalue score bedGraph, condition 2 ChIP treatment against condition 2 control input.

       --s12=ST1T2BDG
              MACS p/qvalue score bedGraph, condition 1 ChIP treatment against condition 2 ChIP treatment.

       --s21=ST2T1BDG
              MACS p/qvalue score bedGraph, condition 2 ChIP treatment against condition 1 ChIP treatment.

       -c CUTOFF, --cutoff=CUTOFF
              Cutoff depends on which method you used for score track. If the file contains p/qvalue scores from
              MACS2, score 5 means p/qvalue 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

bdgdiff 2.0.9.1                                    April 2013                                         BDGDIFF(1)