bdgcmp(1)
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.
