Naive call differential peaks from 4 bedgraph tracks for scores
bdgdiff <--s1 bedGraph> <--s2 bedGraph> <--s12 bedGraph> <--s21 bedGraph> [-c CUTOFF] [-l MIN] [-g MAX] [-o PREFIX]
Call differential regions from four bedGraph files of pair-wise p/qvalue, with customized settings. Please read the descriptions of options carefully.
show program's version number and exit
Show this help message and exit.
MACS p/qvalue score bedGraph, condition 1 ChIP treatment against condition 1 control input.
MACS p/qvalue score bedGraph, condition 2 ChIP treatment against condition 2 control input.
MACS p/qvalue score bedGraph, condition 1 ChIP treatment against condition 2 ChIP treatment.
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