.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.13.
.TH BDGDIFF "1" "December 2012" "bdgdiff 2.0.9.1" "User Commands"
.SH NAME
bdgdiff \- Naive call differential peaks from 4 bedGraph tracks for scores
.SH SYNOPSIS
.B bdgdiff
\fI<--s1 bedGraph> <--s2 bedGraph> <--s12 bedGraph> <--s21 bedGraph> \fR[\fI-c CUTOFF\fR] [\fI-l MIN\fR] [\fI-g MAX\fR] [\fI-o PREFIX\fR]
.SH DESCRIPTION
Call differential regions from four bedGraph files of pair\-wise p/qvalue, with
customized settings. Please read the descriptions of options carefully.
.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\-\-s1\fR=\fIST1C1BDG\fR
MACS p/qvalue score bedGraph, condition 1 ChIP
treatment against condition 1 control input.
.TP
\fB\-\-s2\fR=\fIST2C2BDG\fR
MACS p/qvalue score bedGraph, condition 2 ChIP
treatment against condition 2 control input.
.TP
\fB\-\-s12\fR=\fIST1T2BDG\fR
MACS p/qvalue score bedGraph, condition 1 ChIP
treatment against condition 2 ChIP treatment.
.TP
\fB\-\-s21\fR=\fIST2T1BDG\fR
MACS p/qvalue score bedGraph, condition 2 ChIP
treatment against condition 1 ChIP treatment.
.TP
\fB\-c\fR CUTOFF, \fB\-\-cutoff\fR=\fICUTOFF\fR
Cutoff depends on which method you used for score
track. If the file contains p/qvalue scores from
MACS2, score 5 means p/qvalue 1e\-5. DEFAULT: 5
.TP
\fB\-l\fR MINLEN, \fB\-\-min\-length\fR=\fIMINLEN\fR
minimum length of peak, better to set it as d value.
DEFAULT: 200
.TP
\fB\-g\fR MAXGAP, \fB\-\-max\-gap\fR=\fIMAXGAP\fR
maximum gap between significant points in a peak,
better to set it as tag size. DEFAULT: 30
.TP
\fB\-o\fR OPREFIX, \fB\-\-o\-prefix\fR=\fIOPREFIX\fR
output file prefix, DEFAULT: peak