macs2_bdgpeakcall - Model-based Analysis for ChIP-Sequencing
usage: macs2 bdgpeakcall [-h] -i IFILE [-c CUTOFF] [-l
MINLEN] [-g MAXGAP]
- [--cutoff-analysis] [--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 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
- --cutoff-analysis
- While set, bdgpeakcall will analyze number or total length of peaks that
can be called by different cutoff then output a summary table to help user
decide a better cutoff. Note, minlen and maxgap may affect the results.
DEFAULT: False
- --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.