This is the command macs2_bdgbroadcall 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_bdgbroadcall - Model-based Analysis for ChIP-Sequencing
DESCRIPTION
usage: macs2 bdgbroadcall [-h] -i IFILE [-c CUTOFFPEAK] [-C CUTOFFLINK]
[-l MINLEN] [-g LVL1MAXGAP] [-G LVL2MAXGAP]
[--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 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
--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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