NAME

       mac3_predictd - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

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

       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
              [-g  GSIZE] [-s TSIZE] [--bw BW] [--d-min D_MIN] [-m MFOLD MFOLD] [--outdir OUTDIR]
              [--rfile RFILE] [--buffer-size BUFFER_SIZE] [--verbose VERBOSE]

   options:
       -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. 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
              MACS decide which format the file is.  However, if you want to decide  the  average
              insertion  size/fragment  size  from PE data such as BEDPE or BAMPE, please specify
              the format as BAMPE or BEDPE since MACS3 won't automatically  recognize  three  two
              formats  with  -f AUTO. Please be aware that in PE mode, -g, -s, --bw, --d-min, -m,
              and --rfile have NO effect.  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

       --bw BW
              Band  width  for  picking regions to compute fragment size. This value is only used
              while building the shifting model. DEFAULT: 300

       --d-min D_MIN
              Minimum fragment size in basepair. Any predicted fragment size less than this  will
              be excluded.  DEFAULT: 20

       -m MFOLD MFOLD, --mfold MFOLD MFOLD
              Select  the  regions  within MFOLD range of highconfidence enrichment ratio against
              background to build model. Fold-enrichment in regions  must  be  lower  than  upper
              limit, and higher than the lower limit. Use as "-m 10 30". DEFAULT:5 50

       --outdir OUTDIR
              If  specified  all  output  files  will  be written to that directory. Default: the
              current working directory

       --rfile RFILE
              PREFIX   of   filename   of   R   script   for   drawing   X-correlation    figure.
              DEFAULT:'predictd_model.R' and R file will be predicted_model.R

       --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  of  runtime  message.  0:  only show critical message, 1: show
              additional warning message, 2: show process information, 3:  show  debug  messages.
              DEFAULT:2