Fine-tuning script to call broad peaks from a single bedGraph track for scores
<-i bedGraph> [-c CUTOFF1] [-C CUTOFF2] [-l MIN] [-g MAX1] [-G MAX2] [-o PREFIX]
Call broad peaks from MACS pvalue or qscore score bedGraph output, with
customized settings. Output two files for narrow peaks in encodePeak format,
and one for broad peaks in bed12 format.
show program's version number and exit
- -h, --help
Show this help message and exit.
- -i IFILE, --ifile=IFILE
MACS pvalue score bedGraph
- -c CUTOFFPEAK, --cutoff-peak=CUTOFFPEAK
Cutoff for peaks depending on which method you used
for score track. If the file contains qvalue scores
from MACS2, score 2 means qvalue 0.01. DEFAULT: 2
- -C CUTOFFLINK, --cutoff-link=CUTOFFLINK
Cutoff for linking regions/low abundance regions
depending on which method you used for score track. If
the file contains qvalue scores from MACS2, score 1
means qvalue 0.1, and score 0.3 means qvalue 0.5.
- -l MINLEN, --min-length=MINLEN
minimum length of peak, better to set it as d value.
- -g LVL1MAXGAP, --lvl1-max-gap=LVL1MAXGAP
maximum gap between significant peaks, better to set
it as tag size. DEFAULT: 30
- -G LVL2MAXGAP, --lvl2-max-gap=LVL2MAXGAP
maximum linking between significant peaks, better to
set it as 4 times of d value. DEFAULT: 800
- -o OPREFIX, --o-prefix=OPREFIX
output file prefix, DEFAULT: peak