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.