DESCRIPTION

usage: macs2 filterdup [-h] -i IFILE [IFILE ...]

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

[-g GSIZE] [-s TSIZE] [-p PVALUE] [--keep-dup KEEPDUPLICATES] [--verbose VERBOSE] [--outdir OUTDIR] [-o OUTPUTFILE] [-d]

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.

-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 filterdup' 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

-p PVALUE, --pvalue PVALUE

Pvalue cutoff for binomial distribution test. DEFAULT:1e-5

--keep-dup KEEPDUPLICATES

It controls the 'macs2 filterdup' behavior towards duplicate tags/pairs at the exact same location -- the same coordination and the same strand. The 'auto' option makes 'macs2 filterdup' calculate the maximum tags at the exact same location based on binomal distribution using given -p as pvalue cutoff; and the 'all' option keeps every tags (useful if you only want to convert formats). If an integer is given, at most this number of tags will be kept at the same location. Note, MACS2 callpeak function uses KEEPDUPLICATES=1 as default. Note, if you've used samtools or picard to flag reads as 'PCR/Optical duplicate' in bit 1024, MACS2 will still read them although the reads may be decided by MACS2 as duplicate later. Default: auto

--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 OUTPUTFILE, --ofile OUTPUTFILE

Output BED file name. If not specified, will write to standard output. DEFAULT: stdout

-d, --dry-run

When set, filterdup will only output numbers instead of writing output files, including maximum allowable duplicates, total number of reads before filtering, total number of reads after filtering, and redundant rate. Default: not set