NAME¶
bdgdiff - Naive call differential peaks from 4 bedGraph tracks for scores
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