macs2_pileup - Model-based Analysis for ChIP-Sequencing
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]
- -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