This is the command macs2_bdgpeakcall that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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)
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
--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.
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