bdgdiff1
Naive call differential peaks from 4 bedgraph tracks for scores
Usage
bdgdiff <--s1
bedGraph>
<--s2
bedGraph>
<--s12
bedGraph>
<--s21
bedGraph>
[-c
CUTOFF]
[-l
MIN]
[-g
MAX]
[-o
PREFIX]
Overview
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