NAME¶

macs2 - Model-based Analysis for ChIP-Sequencing

SYNOPSIS¶

macs2 <-t tfile> [-n name] [-g genomesize] [options]

DESCRIPTION¶

Example: macs2 -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01 or example for broad peak calling: macs2 -t ChIP.bam -c Control.bam --broad -g hs macs2 -- Model-based Analysis for ChIP-Sequencing

OPTIONS¶

--version

show program's version number and exit

-h, --help

show this help message and exit.

-t TFILE, --treatment=TFILE

ChIP-seq treatment file. REQUIRED.

-c CFILE, --control=CFILE

Control file.

-n NAME, --name=NAME

Experiment name, which will be used to generate output file names. DEFAULT: "NA"

-f FORMAT, --format=FORMAT

Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or "BOWTIE". The default AUTO option will let MACS decide which format the file is. Please check the definition in 00README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. 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

-s TSIZE, --tsize=TSIZE

Tag size. This will overide the auto detected tag size. DEFAULT: Not set

--bw=BW

Band width. This value is only used while building the shifting model. DEFAULT: 300

-q QVALUE, --qvalue=QVALUE

Minimum FDR (q-value) cutoff for peak detection. DEFAULT: 0.01

-p PVALUE, --pvalue=PVALUE

Pvalue cutoff for peak detection. When set (e.g. -q 0.05 or -q 1e-5), qvalue cutoff will be ignored. Default is not set.

-m MFOLD, --mfold=MFOLD

Select the regions within MFOLD range of highconfidence enrichment ratio against background to build model. The regions must be lower than upper limit, and higher than the lower limit. DEFAULT:10,30

--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.

--auto-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 '--shiftsize' parameter to shift and extend each tags. 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 shiftsize to change it. DEFAULT: False

--shiftsize=SHIFTSIZE

The arbitrary shift size in bp. When nomodel is true, MACS will use this value as 1/2 of fragment size. DEFAULT: 100

--keep-dup=KEEPDUPLICATES

It controls the MACS behavior towards duplicate tags at the exact same location -- the same coordination and the same strand. The default '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. Default: auto

--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

--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. DEFAULT: False

--shift-control

When set, control tags will be shifted just as ChIP tags according to their strand before the extension of d, slocal and llocal. By default, control tags are extended centered at their current positions regardless of strand. You may consider to turn this option on while comparing two ChIP datasets of different condition but the same factor. DEFAULT: False

--half-ext

When set, MACS extends 1/2 d size for each fragment centered at its middle point. DEFAULT: False

-B, --bdg

Whether or not to save extended fragment pileup, local lambda and score tracks at every bp into a bedGraph file. DEFAULT: False

--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

--verbose=VERBOSE

Set verbose level. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2