macs2_callpeak(1) 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] [--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.
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
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
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.
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: 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.
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! 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/
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. DEFAULT: 1000
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. 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
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:

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