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