.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.13.
.TH BDGCMP "1" "December 2012" "bdgcmp 2.0.9.1" "User Commands"
.SH NAME
bdgcmp \- Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias
.SH SYNOPSIS
.B bdgcmp
\fI<-t TREATMENT.BEDGRAPH> <-c CONTROL.BEDGRAPH> <-o OUTPUT.BEDGRAPH> \fR[\fI-m METHOD\fR]
.SH DESCRIPTION
Calculate scores using certain method by comparing a bedGraph file from
treatment and a file from control representing local bias.
.SH OPTIONS
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this help message and exit.
.TP
\fB\-t\fR TFILE, \fB\-\-tfile\fR=\fITFILE\fR
Required: Treatment bedGraph file, e.g.
*_treat_pileup.bdg from MACSv2
.TP
\fB\-c\fR CFILE, \fB\-\-cfile\fR=\fICFILE\fR
Required: Control bedGraph file, e.g.
*_control_lambda.bdg from MACSv2
.TP
\fB\-o\fR OFILE, \fB\-\-output\fR=\fIOFILE\fR
Required: The output bedGraph file to write scores.
.TP
\fB\-m\fR METHOD, \fB\-\-method\fR=\fIMETHOD\fR
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 (\fB\-log10\fR(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.