options:

-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. REQUIRED.

-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}

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. However, if you want to decide the average insertion size/fragment size from PE data such as BEDPE or BAMPE, please specify the format as BAMPE or BEDPE since MACS3 won't automatically recognize three two formats with -f AUTO. Please be aware that in PE mode, -g, -s, --bw, --d-min, -m, and --rfile have NO effect. DEFAULT: "AUTO"

-g GSIZE, --gsize GSIZE

Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse (2,652,783,500), 'ce' for C. elegans (100,286,401) and 'dm' for fruitfly (142,573,017), Default:hs. The effective genome size numbers for the above four species are collected from Deeptools https: //deeptools.readthedocs.io/en/develop/content/feature/ effectiveGenomeSize.html Please refer to deeptools to define the best genome size you plan to use.

-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

--d-min D_MIN

Minimum fragment size in basepair. Any predicted fragment size less than this will be excluded. DEFAULT: 20

-m MFOLD MFOLD, --mfold MFOLD MFOLD

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_model.R' and R file will be predicted_model.R

--buffer-size BUFFER_SIZE

Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter. However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to decrease memory usage (but it will take longer time to read alignment files). Minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000

--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