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,BAMPE,BEDPE}]
              [-B] [--extsize EXTSIZE] [--buffer-size BUFFER_SIZE] [--verbose VERBOSE]

   options:
       -h, --help
              show this help message and exit

       -i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
              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,BAMPE,BEDPE},      --format
       {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}
              Format of tag file, "AUTO", "BED",  "ELAND",  "ELANDMULTI",  "ELANDEXPORT",  "SAM",
              "BAM",  "BOWTIE",  "BAMPE",  or  "BEDPE".  The  default AUTO option will let 'macs2
              pileup' decide which format the file is.  DEFAULT: "AUTO", MACS2 will pick a format
              from   "AUTO",  "BED",  "ELAND",  "ELANDMULTI",  "ELANDEXPORT",  "SAM",  "BAM"  and
              "BOWTIE". If the format is BAMPE or BEDPE, please  specify  it  explicitly.  Please
              note  that when the format is BAMPE or BEDPE, the -B and --extsize options would be
              ignored.

       -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. This option will be
              ignored when the format is set as BAMPE or BEDPE. 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. This option will be ignored when the format is set as BAMPE
              or BEDPE.  DEFAULT: 200

       --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.  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