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.