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

macs2_pileup 2.1.1.20160309                       February 2018                                  MACS2_PILEUP(1)