NAME

       macs2_filterdup - Model-based Analysis for ChIP-Sequencing

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

macs2_filterdup 2.1.1.20160309                    February 2018                               MACS2_FILTERDUP(1)