xenial (1) macs2_pileup.1.gz

Provided by: macs_2.1.0.20151222-1_amd64 bug

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