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MACS2_CALLPEAK(1) |
User Commands |
MACS2_CALLPEAK(1) |
NAME¶
macs2_callpeak - 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
- -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