macs2_bdgpeakcall(1) 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)

optional arguments:

-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
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
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.