SYNOPSIS

bdgdiff <--s1 bedGraph> <--s2 bedGraph> <--s12 bedGraph> <--s21 bedGraph> [-c CUTOFF] [-l MIN] [-g MAX] [-o PREFIX]

DESCRIPTION

Call differential regions from four bedGraph files of pair-wise p/qvalue, with customized settings. Please read the descriptions of options carefully.

OPTIONS

--version

show program's version number and exit

-h, --help

Show this help message and exit.

--s1=ST1C1BDG

MACS p/qvalue score bedGraph, condition 1 ChIP treatment against condition 1 control input.

--s2=ST2C2BDG

MACS p/qvalue score bedGraph, condition 2 ChIP treatment against condition 2 control input.

--s12=ST1T2BDG

MACS p/qvalue score bedGraph, condition 1 ChIP treatment against condition 2 ChIP treatment.

--s21=ST2T1BDG

MACS p/qvalue score bedGraph, condition 2 ChIP treatment against condition 1 ChIP treatment.

-c CUTOFF, --cutoff=CUTOFF

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

-l MINLEN, --min-length=MINLEN

minimum length of peak, better to set it as d value. DEFAULT: 200

-g MAXGAP, --max-gap=MAXGAP

maximum gap between significant points in a peak, better to set it as tag size. DEFAULT: 30

-o OPREFIX, --o-prefix=OPREFIX

output file prefix, DEFAULT: peak