bdgpeakcall1
Naive call peaks from a single bedgraph track for scores
Usage
bdgpeakcall <-i
bedGraph>
[-c
CUTOFF]
[-l
MIN]
[-g
MAX]
[-o
PREFIX]
Overview
Call peaks from MACS pvalue or qscore score bedGraph output, with customized settings. Output encodePeak format peaks, combining peak boundaries, peak summits.
Options
-
--version -
show program's version number and exit
-
-h, --help -
Show this help message and exit.
-
-i IFILE, --ifile=IFILE -
MACS pvalue score bedGraph
-
-c CUTOFF, --cutoff=CUTOFF -
Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 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