NAME

       mac3_filterdup - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs3 filterdup [-h] -i IFILE [IFILE ...]

       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
              [-g  GSIZE]  [-s  TSIZE]  [-p  PVALUE]  [--keep-dup  KEEPDUPLICATES] [--buffer-size
              BUFFER_SIZE] [--verbose VERBOSE] [--outdir OUTDIR] [-o OUTPUTFILE] [-d]

   options:
       -h, --help
              show this help message and exit

       -i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
              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
              'macs3 filterdup' decide which format the file is. Please check the  definition  in
              README   file   if   you   choose   ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE  or
              BAMPE/BEDPE. 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

       -p PVALUE, --pvalue PVALUE
              Pvalue cutoff for binomial distribution test.  DEFAULT:1e-5

       --keep-dup KEEPDUPLICATES
              It  controls  the  'macs3  filterdup'  behavior towards duplicate tags/pairs at the
              exact same location -- the same coordination and the same strand. The 'auto' option
              makes 'macs3 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,  MACS3  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, MACS3 will  still  read  them
              although the reads may be decided by MACS3 as duplicate later. Default: auto

       --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 OUTPUTFILE, --ofile OUTPUTFILE
              Output BED file name. If not specified, will write to standard output. Note, if the
              input format is BAMPE or BEDPE, the output will be in BEDPE format. 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