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

macs2_predictd 2.1.0.20151222                     February 2016                                MACS2_PREDICTD(1)