macs2_callpeak(1)
Model-based Analysis for ChIP-Sequencing
DESCRIPTION
usage: macs2 callpeak [-h]
-t TFILE [TFILE ...] [-c [CFILE [CFILE ...]]]
- [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
-
[-g GSIZE] [--keep-dup KEEPDUPLICATES]
[--buffer-size BUFFER_SIZE] [--outdir OUTDIR] [-n NAME]
[-B] [--verbose VERBOSE] [--trackline] [--SPMR]
[-s TSIZE] [--bw BW] [-m MFOLD MFOLD] [--fix-bimodal]
[--nomodel] [--shift SHIFT] [--extsize EXTSIZE]
[-q QVALUE | -p PVALUE] [--to-large] [--ratio RATIO]
[--down-sample] [--seed SEED] [--tempdir TEMPDIR]
[--nolambda] [--slocal SMALLLOCAL] [--llocal LARGELOCAL]
[--broad] [--broad-cutoff BROADCUTOFF]
[--cutoff-analysis] [--call-summits]
[--fe-cutoff FECUTOFF]
optional arguments:
- -h, --help
-
show this help message and exit
Input files arguments:
- -t TFILE [TFILE ...], --treatment TFILE [TFILE ...]
-
ChIP-seq treatment file. If multiple files are given
as '-t A B C', then they will all be read and pooled
together. REQUIRED.
- -c [CFILE [CFILE ...]], --control [CFILE [CFILE ...]]
-
Control file. If multiple files are given as '-c A B
C', they will be pooled to estimate ChIP-seq
background noise.
- -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" or "ELAND" or
"ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or
"BOWTIE" or "BAMPE" or "BEDPE". The default AUTO
option will let MACS decide which format (except for
BAMPE and BEDPE which should be implicitly set) the
file is. Please check the definition in README. Please
note that if the format is set as BAMPE or BEDPE,
MACS2 will call its special Paired-end mode to call
peaks by piling up the actual ChIPed fragments defined
by both aligned ends, instead of predicting the
fragment size first and extending reads. Also please
note that the BEDPE only contains three columns, and
is NOT the same BEDPE format used by BEDTOOLS.
DEFAULT: "AUTO"
- -g GSIZE, --gsize GSIZE
-
Effective genome size. It can be 1.0e+9 or 1000000000,
or shortcuts:'hs' for human (2.7e9), 'mm' for mouse
(1.87e9), 'ce' for C. elegans (9e7) and 'dm' for
fruitfly (1.2e8), Default:hs
- --keep-dup KEEPDUPLICATES
-
It controls the MACS behavior towards duplicate tags
at the exact same location -- the same coordination
and the same strand. The 'auto' option makes MACS
calculate the maximum tags at the exact same location
based on binomal distribution using 1e-5 as pvalue
cutoff; and the 'all' option keeps every tags. If an
integer is given, at most this number of tags will be
kept at the same location. Note, if you've used
samtools or picard to flag reads as 'PCR/Optical
duplicate' in bit 1024, MACS2 will still read them
although the reads may be decided by MACS2 as
duplicate later. The default is to keep one tag at the
same location. Default: 1
- --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 * 2 Bytes. DEFAULT: 100000
Output arguments:
- --outdir OUTDIR
-
If specified all output files will be written to that
directory. Default: the current working directory
- -n NAME, --name NAME
-
Experiment name, which will be used to generate output
file names. DEFAULT: "NA"
- -B, --bdg
-
Whether or not to save extended fragment pileup, and
local lambda tracks (two files) at every bp into a
bedGraph file. DEFAULT: False
- --verbose VERBOSE
-
Set verbose level of runtime message. 0: only show
critical message, 1: show additional warning message,
2: show process information, 3: show debug messages.
DEFAULT:2
- --trackline
-
Tells MACS to include trackline with bedGraph files.
To include this trackline while displaying bedGraph at
UCSC genome browser, can show name and description of
the file as well. However my suggestion is to convert
bedGraph to bigWig, then show the smaller and faster
binary bigWig file at UCSC genome browser, as well as
downstream analysis. Require -B to be set. Default:
Not include trackline.
- --SPMR
-
If True, MACS will save signal per million reads for
fragment pileup profiles. Require -B to be set.
Default: False
Shifting model arguments:
- -s TSIZE, --tsize TSIZE
-
Tag size. This will override the auto detected tag
size. DEFAULT: Not set
- --bw BW
-
Band width for picking regions to compute fragment
size. This value is only used while building the
shifting model. DEFAULT: 300
- -m MFOLD MFOLD, --mfold MFOLD MFOLD
-
Select the regions within MFOLD range of highconfidence enrichment ratio against background to
build model. Fold-enrichment in regions must be lower
than upper limit, and higher than the lower limit. Use
as "-m 10 30". DEFAULT:5 50
- --fix-bimodal
-
Whether turn on the auto pair model process. If set,
when MACS failed to build paired model, it will use
the nomodel settings, the --exsize parameter to extend
each tags towards 3' direction. Not to use this
automate fixation is a default behavior now. DEFAULT:
False
- --nomodel
-
Whether or not to build the shifting model. If True,
MACS will not build model. by default it means
shifting size = 100, try to set extsize to change it.
DEFAULT: False
- --shift SHIFT
-
(NOT the legacy --shiftsize option!) The arbitrary
shift in bp. Use discretion while setting it other
than default value. When NOMODEL is set, MACS will use
this value to move cutting ends (5') towards 5'->3'
direction then apply EXTSIZE to extend them to
fragments. When this value is negative, ends will be
moved toward 3'->5' direction. Recommended to keep it
as default 0 for ChIP-Seq datasets, or -1 * half of
EXTSIZE together with EXTSIZE option for detecting
enriched cutting loci such as certain DNAseI-Seq
datasets. Note, you can't set values other than 0 if
format is BAMPE or BEDPE for paired-end data. DEFAULT:
0.
- --extsize EXTSIZE
-
The arbitrary extension size in bp. When nomodel is
true, MACS will use this value as fragment size to
extend each read towards 3' end, then pile them up.
It's exactly twice the number of obsolete SHIFTSIZE.
In previous language, each read is moved 5'->3'
direction to middle of fragment by 1/2 d, then
extended to both direction with 1/2 d. This is
equivalent to say each read is extended towards 5'->3'
into a d size fragment. DEFAULT: 200. EXTSIZE and
SHIFT can be combined when necessary. Check SHIFT
option.
Peak calling arguments:
- -q QVALUE, --qvalue QVALUE
-
Minimum FDR (q-value) cutoff for peak detection.
DEFAULT: 0.05. -q, and -p are mutually exclusive.
- -p PVALUE, --pvalue PVALUE
-
Pvalue cutoff for peak detection. DEFAULT: not set.
-q, and -p are mutually exclusive. If pvalue cutoff is
set, qvalue will not be calculated and reported as -1
in the final .xls file.
- --to-large
-
When set, scale the small sample up to the bigger
sample. By default, the bigger dataset will be scaled
down towards the smaller dataset, which will lead to
smaller p/qvalues and more specific results. Keep in
mind that scaling down will bring down background
noise more. DEFAULT: False
- --ratio RATIO
-
When set, use a custom scaling ratio of ChIP/control
(e.g. calculated using NCIS) for linear scaling.
DEFAULT: ingore
- --down-sample
-
When set, random sampling method will scale down the
bigger sample. By default, MACS uses linear scaling.
Warning: This option will make your result unstable
and irreproducible since each time, random reads would
be selected. Consider to use 'randsample' script
instead. <not implmented>If used together with --SPMR,
1 million unique reads will be randomly picked.</not
implemented> Caution: due to the implementation, the
final number of selected reads may not be as you
expected! DEFAULT: False
- --seed SEED
-
Set the random seed while down sampling data. Must be
a non-negative integer in order to be effective.
DEFAULT: not set
- --tempdir TEMPDIR
-
Optional directory to store temp files. DEFAULT: ,/tmp/
- --nolambda
-
If True, MACS will use fixed background lambda as
local lambda for every peak region. Normally, MACS
calculates a dynamic local lambda to reflect the local
bias due to potential chromatin structure.
- --slocal SMALLLOCAL
-
The small nearby region in basepairs to calculate
dynamic lambda. This is used to capture the bias near
the peak summit region. Invalid if there is no control
data. If you set this to 0, MACS will skip slocal
lambda calculation. *Note* that MACS will always
perform a d-size local lambda calculation. The final
local bias should be the maximum of the lambda value
from d, slocal, and llocal size windows. DEFAULT: 1000
- --llocal LARGELOCAL
-
The large nearby region in basepairs to calculate
dynamic lambda. This is used to capture the surround
bias. If you set this to 0, MACS will skip llocal
lambda calculation. *Note* that MACS will always
perform a d-size local lambda calculation. The final
local bias should be the maximum of the lambda value
from d, slocal, and llocal size windows. DEFAULT:
10000.
- --broad
-
If set, MACS will try to call broad peaks by linking
nearby highly enriched regions. The linking region is
controlled by another cutoff through --linking-cutoff.
The maximum linking region length is 4 times of d from
MACS. DEFAULT: False
- --broad-cutoff BROADCUTOFF
-
Cutoff for broad region. This option is not available
unless --broad is set. If -p is set, this is a pvalue
cutoff, otherwise, it's a qvalue cutoff. DEFAULT: 0.1
- --cutoff-analysis
-
While set, MACS2 will analyze number or total length
of peaks that can be called by different p-value
cutoff then output a summary table to help user decide
a better cutoff. The table will be saved in
NAME_cutoff_analysis.txt file. Note, minlen and maxgap
may affect the results. WARNING: May take ~30 folds
longer time to finish. DEFAULT: False
Post-processing options:
- --call-summits
-
If set, MACS will use a more sophisticated signal
processing approach to find subpeak summits in each
enriched peak region. DEFAULT: False
- --fe-cutoff FECUTOFF
-
When set, the value will be used to filter out peaks
with low fold-enrichment. Note, MACS2 use 1.0 as
pseudocount while calculating fold-enrichment.
DEFAULT: 1.0