NAME

       bdgcmp  -  Calculate  scores  using certain method by comparing a bedGraph file from treatment and a file
       from control representing local bias

SYNOPSIS

       bdgcmp <-t TREATMENT.BEDGRAPH> <-c CONTROL.BEDGRAPH> <-o OUTPUT.BEDGRAPH> [-m METHOD]

DESCRIPTION

       Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control
       representing local bias.

OPTIONS

       --version
              show program's version number and exit

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

       -t TFILE, --tfile=TFILE
              Required: Treatment bedGraph file, e.g.  *_treat_pileup.bdg from MACSv2

       -c CFILE, --cfile=CFILE
              Required: Control bedGraph file, e.g.  *_control_lambda.bdg from MACSv2

       -o OFILE, --output=OFILE
              Required: The output bedGraph file to write scores.

       -m METHOD, --method=METHOD
              Method to use while calculating a score in any bin by comparing treatment value and control value.
              Available choices are: ppois, substract, divide which  represent  Poisson  Pvalue  (-log10(pvalue)
              form)  using  control  as  lambda  and treatment as observation, substraction from treatment, fold
              change which may be problematic if there are zero in control. Default option is ppois.

bdgcmp 2.0.9.1                                     April 2013                                          BDGCMP(1)