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

macs2 predictd 2.2.7.1                             April 2022                                  MACS2_PREDICTD(1)