xenial (1) macs2_filterdup.1.gz

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 duplicates in bit 1024, MACS2 will  discard  them  no  matter  how  you  set  KEEPDUPLICATES.
              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