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