bdgcmp1
Calculate scores using certain method by comparing a bedgraph file from treatment and a file from control representing local bias
Usage
bdgcmp <-t
TREATMENT.BEDGRAPH>
<-c
CONTROL.BEDGRAPH>
<-o
OUTPUT.BEDGRAPH>
[-m
METHOD]
Overview
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.