Provided by: macs_2.0.9.1-1_amd64 
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
macs2 2.0.9.1 April 2013 MACS2(1)