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macs2_callpeak - Model-based Analysis for ChIP-Sequencing


usage: macs2 callpeak [-h] -t TFILE [TFILE ...] [-c [CFILE [CFILE ...]]]

[-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] [--nolambda] [--slocal SMALLLOCAL] [--llocal LARGELOCAL] [--broad]
[--broad-cutoff BROADCUTOFF] [--cutoff-analysis] [--call-summits] [--fe-cutoff

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.

Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or
"SAM" or "BAM" or "BOWTIE" or "BAMPE". The default AUTO option will let MACS decide
which format the file is. Please check the definition in README file if you choose

-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

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. 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.

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

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

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

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:

--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 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.

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

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!

--seed SEED
Set the random seed while down sampling data. Must be a non-negative integer in
order to be effective. DEFAULT: not set

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.

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.

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.

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.

--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

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.

Post-processing options:
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

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