options:

-h, --help

show this help message and exit

-b BEDFILE

Candidate peak file in BED format. REQUIRED.

-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.

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

Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or "BOWTIE". The default AUTO option will let 'macs2 refinepeak' decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: "AUTO"

-c CUTOFF, --cutoff CUTOFF

Cutoff DEFAULT: 5

-w WINDOWSIZE, --window-size WINDOWSIZE

Scan window size on both side of the summit (default: 100bp)

--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. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. If you want to know where are the duplicate reads, use 3. DEFAULT:2

--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.