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,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. Note that pair-end data is not supposed to work with this
              command. 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.  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

       --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'
              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