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MACS2_BDGBROADCALL(1) User Commands MACS2_BDGBROADCALL(1)

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]
[--no-trackline] [--outdir OUTDIR] (-o OFILE | --o-prefix OPREFIX)

options:

show this help message and exit
MACS score in bedGraph. REQUIRED
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
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
minimum length of peak, better to set it as d value. DEFAULT: 200
maximum gap between significant peaks, better to set it as tag size. DEFAULT: 30
maximum linking between significant peaks, better to set it as 4 times of d value. DEFAULT: 800
Tells MACS not to include trackline with bedGraph files. The trackline is required by UCSC.
If specified all output files will be written to that directory. Default: the current working directory
Output file name. Mutually exclusive with --o-prefix.
Output file prefix. Mutually exclusive with -o/--ofile.
January 2023 macs2 bdgbroadcall 2.2.7.1