NAME

       macs2_pileup - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs2 pileup [-h] -i IFILE [IFILE ...] -o OUTPUTFILE [--outdir OUTDIR]

       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}]
              [-B] [--extsize EXTSIZE] [--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.

       -o OUTPUTFILE, --ofile OUTPUTFILE
              Output  bedGraph  file  name.  If  not  specified,  will  write to standard output.
              REQUIRED.

       --outdir OUTDIR
              If specified all output files will be  written  to  that  directory.  Default:  the
              current working directory

       -f             {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE},            --format
       {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}
              Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI"  or  "ELANDEXPORT"  or
              "SAM"  or "BAM" or "BOWTIE". The default AUTO option will let 'macs2 pileup' decide
              which format the file is. Please check the definition in README file if you  choose
              ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: "AUTO"

       -B, --both-direction
              By  default,  any  read  will be extended towards downstream direction by extension
              size.  So  it's  [0,size-1]  (1-based  index  system)  for  plus  strand  read  and
              [-size+1,0]  for  minus strand read where position 0 is 5' end of the aligned read.
              Default behavior can simulate MACS2 way  of  piling  up  ChIP  sample  reads  where
              extension  size  is  set  as  fragment size/d. If this option is set as on, aligned
              reads will be extended in both upstream  and  downstream  directions  by  extension
              size.  It  means  [-size,size]  where  0  is  the  5' end of a aligned read. It can
              partially simulate MACS2 way of piling up control reads. However MACS2  local  bias
              is  calculated  by  maximizing  the  expected  pileup  over  a ChIP fragment size/d
              estimated from 10kb, 1kb, d and whole genome background. DEFAULT: False

       --extsize EXTSIZE
              The extension size in bps. Each alignment read will become a EXTSIZE  of  fragment,
              then  be  piled up. Check description for -B for detail. It's twice the `shiftsize`
              in old MACSv1 language. DEFAULT: 200

       --verbose VERBOSE
              Set verbose level. 0: only  show  critical  message,  1:  show  additional  warning
              message,  2:  show process information, 3: show debug messages. If you want to know
              where are the duplicate reads, use 3. DEFAULT:2