macs2_bdgbroadcall - Model-based Analysis for ChIP-Sequencing
usage: macs2 bdgbroadcall [-h] -i IFILE [-c CUTOFFPEAK] [-C
CUTOFFLINK]
- [-l MINLEN] [-g LVL1MAXGAP] [-G LVL2MAXGAP]
- [--no-trackline] [--outdir OUTDIR] (-o OFILE | --o-prefix
OPREFIX)
- -h, --help
- show this help message and exit
- -i IFILE, --ifile
IFILE
- MACS score in bedGraph. REQUIRED
- -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. DEFAULT: 1
- -l MINLEN,
--min-length MINLEN
- minimum length of peak, better to set it as d value. DEFAULT: 200
- -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
- --no-trackline
- Tells MACS not to include trackline with bedGraph files. The trackline is
required by UCSC.
- --outdir
OUTDIR
- If specified all output files will be written to that directory. Default:
the current working directory
- -o OFILE, --ofile
OFILE
- Output file name. Mutually exclusive with --o-prefix.
- --o-prefix
OPREFIX
- Output file prefix. Mutually exclusive with -o/--ofile.