NAME
macs2_bdgpeakcall - Model-based Analysis for ChIP-Sequencing
DESCRIPTION
usage: macs2 bdgpeakcall [-h] -i IFILE [-c CUTOFF] [-l MINLEN] [-g MAXGAP]
- [--cutoff-analysis] [--no-trackline]
-
[--outdir OUTDIR] (-o OFILE | --o-prefix OPREFIX)
options:
- -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.