Provided by: macs_3.0.1-2build1_amd64 
NAME
mac3_callpeak - Model-based Analysis for ChIP-Sequencing
DESCRIPTION
usage: macs3 callpeak [-h] -t TFILE [TFILE ...] [-c [CFILE ...]]
[-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
[-g GSIZE] [-s TSIZE] [--keep-dup KEEPDUPLICATES] [--outdir OUTDIR] [-n NAME] [-B]
[--verbose VERBOSE] [--trackline] [--SPMR] [--nomodel] [--shift SHIFT] [--extsize
EXTSIZE] [--bw BW] [--d-min D_MIN] [-m MFOLD MFOLD] [--fix-bimodal] [-q QVALUE | -p
PVALUE] [--scale-to {large,small}] [--down-sample] [--seed SEED] [--tempdir
TEMPDIR] [--nolambda] [--slocal SMALLLOCAL] [--llocal LARGELOCAL] [--max-gap
MAXGAP] [--min-length MINLEN] [--broad] [--broad-cutoff BROADCUTOFF]
[--cutoff-analysis] [--call-summits] [--fe-cutoff FECUTOFF] [--to-large] [--ratio
RATIO] [--buffer-size BUFFER_SIZE]
options:
-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 ...], --control [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, MACS3 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
(2,913,022,398), 'mm' for mouse (2,652,783,500), 'ce' for C. elegans (100,286,401)
and 'dm' for fruitfly (142,573,017), Default:hs. The effective genome size numbers
for the above four species are collected from Deeptools https:
//deeptools.readthedocs.io/en/develop/content/feature/ effectiveGenomeSize.html
Please refer to deeptools to define the best genome size you plan to use.
-s TSIZE, --tsize TSIZE
Tag size/read length. This will override the auto detected tag size. DEFAULT: Not
set
--keep-dup KEEPDUPLICATES
It controls the 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, MACS3 will
still read them although the reads may be decided by MACS3 as duplicate later. If
you plan to rely on samtools/picard/any other tool to filter duplicates, please
remove those duplicate reads and save a new alignment file then ask MACS3 to keep
all by '--keep-dup all'. The default is to keep one tag at the same location.
Default: 1
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. It
won't interfere with computing pvalue/qvalue during peak calling, since internally
MACS3 keeps using the raw pileup and scaling factors between larger and smaller
dataset to calculate statistics measurements. If you plan to use the signal output
in bedGraph to call peaks using bdgcmp and bdgpeakcall, you shouldn't use this
option because you will end up with different results. However, this option is
recommended for displaying normalized pileup tracks across many datasets. Require
-B to be set. Default: False
Shifting model arguments:
--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. It's highly
recommended that while you have many datasets to process and you plan to compare
different conditions, aka differential calling, use both 'nomodel' and 'extsize' to
make signal files from different datasets comparable. 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.
--bw BW
Band width for picking regions to compute fragment size. This value is only used
while building the shifting model. Tweaking this is not recommended. DEFAULT: 300
--d-min D_MIN
Minimum fragment size in basepair. Any predicted fragment size less than this will
be excluded. DEFAULT: 20
-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". This setting is only
used while building the shifting model. Tweaking it is not recommended. 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
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.
--scale-to {large,small}
When set to 'small', scale the larger sample up to the smaller sample. When set to
'larger', scale the smaller sample up to the bigger sample. By default, scale to
'small'. This option replaces the obsolete ' --to-large' option. The default
behavior is recommended since it will lead to less significant p/q-values in
general but more specific results. Keep in mind that scaling down will influence
control/input sample more. DEFAULT: 'small', the choice is either 'small' or
'large'.
--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 the potential chromatin accessibility.
--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 while the control data is
available. The final local bias would be the maximum of the lambda value from d,
slocal, and llocal size windows. While control is not available, d and slocal
lambda won't be considered. 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
while the control data is available. The final local bias would be the maximum of
the lambda value from d, slocal, and llocal size windows. While control is not
available, d and slocal lambda won't be considered. DEFAULT: 10000.
--max-gap MAXGAP
Maximum gap between significant sites to cluster them together. The DEFAULT value
is the detected read length/tag size.
--min-length MINLEN
Minimum length of a peak. The DEFAULT value is the predicted fragment size d. Note,
if you set a value smaller than the fragment size, it may have NO effect on the
result. For BROAD peak calling, try to set a large value such as 500bps. You can
also use '-- cutoff-analysis' option with default setting, and check the column
'avelpeak' under different cutoff values to decide a reasonable minlen value.
--broad
If set, MACS will try to call broad peaks using the --broad-cutoff setting. Please
tweak '--broad-cutoff' setting to control the peak calling behavior. At the
meantime, either -q or -p cutoff will be used to define regions with 'stronger
enrichment' inside of broad peaks. The maximum gap is expanded to 4 * MAXGAP
(--max-gap parameter). As a result, MACS will output a 'gappedPeak' and a
'broadPeak' file instead of 'narrowPeak' file. Note, a broad peak will be reported
even if there is no 'stronger enrichment' inside. 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. Please note that
in broad peakcalling mode, MACS3 uses this setting to control the overall peak
calling behavior, then uses -q or -p setting to define regions inside broad region
as 'stronger' enrichment. DEFAULT: 0.1
--cutoff-analysis
While set, MACS3 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.
The result can be useful for users to decide a reasonable cutoff value. 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 as the minimum requirement to filter out peaks
with low foldenrichment. Note, MACS3 adds one as pseudocount while calculating
fold-enrichment. By default, it is set as 1 so there is no filtering. DEFAULT: 1.0
Obsolete options:
--to-large
Obsolete option. Please use '--scale-to large' instead.
--ratio RATIO
Obsolete option. Originally designed to normalize treatment and control with
customized ratio, now it won't have any effect.
Other options:
--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
EXAMPLES
1. Peak calling for regular TF ChIP-seq:
$ macs3 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01
2. Broad peak calling on Histone Mark ChIP-seq:
$ macs3 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1
3. Peak calling on ATAC-seq (paired-end mode):
$ macs3 callpeak -f BAMPE -t ATAC.bam -g hs -n test -B -q 0.01
4. Peak calling on ATAC-seq ( focusing on insertion sites, and using single-end mode):
$ macs3 callpeak -f BAM -t ATAC.bam -g hs -n test -B -q 0.01 --shift -50
--extension 100