xenial (1) macs2_predictd.1.gz

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