Calculate scores using certain method by comparing a bedgraph file from treatment and a file from control representing local bias
bdgcmp <-t TREATMENT.BEDGRAPH> <-c CONTROL.BEDGRAPH> <-o OUTPUT.BEDGRAPH> [-m METHOD]
Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias.
--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.