NAME

       macs2_predictd - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

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

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

   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,BAMPE},          --format
       {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE}
              Format  of  tag  file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or
              "SAM" or "BAM" or "BOWTIE". The default AUTO option  will  let  MACS  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

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

       -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'
              and R file will be predicted_model.R

       --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