NAME

       mac3_pileup - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs3 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. 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  'macs3
              pileup' decide which format the file is.  DEFAULT: "AUTO", MACS3 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 MACS3 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 MACS3 way of piling up control reads. However MACS3  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