Ubuntu Manpage: macs2 - Model-based Analysis for ChIP-Sequencing

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