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MACS2_PILEUP(1) |
User Commands |
MACS2_PILEUP(1) |
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