macs3_bdgbroadcall1

options:

-h, --help

show this help message and exit

-i, --ifile IFILE

MACS score in bedGraph. REQUIRED

-c, --cutoff-peak CUTOFFPEAK

Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS3, score 2 means qvalue 0.01. Regions with signals lower than cutoff will not be considerred as enriched regions. DEFAULT: 2

-C, --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 MACS3, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1

-l, --min-length MINLEN

minimum length of peak, better to set it as d value. DEFAULT: 200

-g, --lvl1-max-gap LVL1MAXGAP

maximum gap between significant peaks, better to set it as tag size. DEFAULT: 30

-G, --lvl2-max-gap LVL2MAXGAP

maximum linking between significant peaks, better to set it as 4 times of d value. DEFAULT: 800

--no-trackline

Tells MACS not to include trackline with bedGraph files. The trackline is required by UCSC.

--verbose VERBOSE

Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2

--outdir OUTDIR

If specified all output files will be written to that directory. Default: the current working directory

-o, --ofile OFILE

Output file name. Mutually exclusive with --o-prefix.

--o-prefix OPREFIX

Output file prefix. Mutually exclusive with -o/--ofile.