macs2_predictd(1) Model-based Analysis for ChIP-Sequencing


usage: macs2 predictd [-h] -i IFILE [IFILE ...]
[-g GSIZE] [-s TSIZE] [--bw BW] [-m MFOLD MFOLD] [--outdir OUTDIR] [--rfile RFILE] [--verbose VERBOSE]

optional arguments:

-h, --help
show this help message and exit
-i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
ChIP-seq alignment file. If multiple files are given as '-t A B C', then they will all be read and combined. Note that pair-end data is not supposed to work with this command. REQUIRED.
Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or "BOWTIE" or "BAMPE" or "BEDPE". The default AUTO option will let MACS decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: "AUTO"
-g GSIZE, --gsize GSIZE
Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs
-s TSIZE, --tsize TSIZE
Tag size. This will override the auto detected tag size. DEFAULT: Not set
--bw BW
Band width for picking regions to compute fragment size. This value is only used while building the shifting model. DEFAULT: 300
Select the regions within MFOLD range of highconfidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than upper limit, and higher than the lower limit. Use as "-m 10 30". DEFAULT:5 50
--outdir OUTDIR
If specified all output files will be written to that directory. Default: the current working directory
--rfile RFILE
PREFIX of filename of R script for drawing X-correlation figure. DEFAULT:'predictd' and R file will be predicted_model.R
--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