.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.13.
.TH MACS2 "1" "December 2012" "macs2 2.0.9.1" "User Commands"
.SH NAME
macs2 \- Model-based Analysis for ChIP-Sequencing
.SH SYNOPSIS
.B macs2
\fI<-t tfile> \fR[\fI-n name\fR] [\fI-g genomesize\fR] [\fIoptions\fR]
.SH DESCRIPTION
Example: macs2 \fB\-t\fR ChIP.bam \fB\-c\fR Control.bam \fB\-f\fR BAM \fB\-g\fR hs \fB\-n\fR test \fB\-B\fR \fB\-q\fR 0.01
.PP
or example for broad peak calling: macs2 \fB\-t\fR ChIP.bam \fB\-c\fR Control.bam \fB\-\-broad\fR \fB\-g\fR hs
.PP
macs2 \fB\-\-\fR Model\-based Analysis for ChIP\-Sequencing
.SH OPTIONS
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit.
.TP
\fB\-t\fR TFILE, \fB\-\-treatment\fR=\fITFILE\fR
ChIP\-seq treatment file. REQUIRED.
.TP
\fB\-c\fR CFILE, \fB\-\-control\fR=\fICFILE\fR
Control file.
.TP
\fB\-n\fR NAME, \fB\-\-name\fR=\fINAME\fR
Experiment name, which will be used to generate output
file names. DEFAULT: "NA"
.TP
\fB\-f\fR FORMAT, \fB\-\-format\fR=\fIFORMAT\fR
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"
.TP
\fB\-g\fR GSIZE, \fB\-\-gsize\fR=\fIGSIZE\fR
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
.TP
\fB\-s\fR TSIZE, \fB\-\-tsize\fR=\fITSIZE\fR
Tag size. This will overide the auto detected tag
size. DEFAULT: Not set
.TP
\fB\-\-bw\fR=\fIBW\fR
Band width. This value is only used while building the
shifting model. DEFAULT: 300
.TP
\fB\-q\fR QVALUE, \fB\-\-qvalue\fR=\fIQVALUE\fR
Minimum FDR (q\-value) cutoff for peak detection.
DEFAULT: 0.01
.TP
\fB\-p\fR PVALUE, \fB\-\-pvalue\fR=\fIPVALUE\fR
Pvalue cutoff for peak detection. When set (e.g. \fB\-q\fR
0.05 or \fB\-q\fR 1e\-5), qvalue cutoff will be ignored.
Default is not set.
.TP
\fB\-m\fR MFOLD, \fB\-\-mfold\fR=\fIMFOLD\fR
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
.TP
\fB\-\-nolambda\fR
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.
.TP
\fB\-\-slocal\fR=\fISMALLLOCAL\fR
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
.TP
\fB\-\-llocal\fR=\fILARGELOCAL\fR
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.
.TP
\fB\-\-auto\-bimodal\fR
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
.TP
\fB\-\-nomodel\fR
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
.TP
\fB\-\-shiftsize\fR=\fISHIFTSIZE\fR
The arbitrary shift size in bp. When nomodel is true,
MACS will use this value as 1/2 of fragment size.
DEFAULT: 100
.TP
\fB\-\-keep\-dup\fR=\fIKEEPDUPLICATES\fR
It controls the MACS behavior towards duplicate tags
at the exact same location \fB\-\-\fR 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
.TP
\fB\-\-to\-large\fR
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
.TP
\fB\-\-down\-sample\fR
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
.TP
\fB\-\-shift\-control\fR
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
.TP
\fB\-\-half\-ext\fR
When set, MACS extends 1/2 d size for each fragment
centered at its middle point. DEFAULT: False
.TP
\fB\-B\fR, \fB\-\-bdg\fR
Whether or not to save extended fragment pileup, local
lambda and score tracks at every bp into a bedGraph
file. DEFAULT: False
.TP
\fB\-\-broad\fR
If set, MACS will try to call broad peaks by linking
nearby highly enriched regions. The linking region is
controlled by another cutoff through \fB\-\-linking\-cutoff\fR.
The maximum linking region length is 4 times of d from
MACS. DEFAULT: False
.TP
\fB\-\-broad\-cutoff\fR=\fIBROADCUTOFF\fR
Cutoff for broad region. This option is not available
unless \fB\-\-broad\fR is set. If \fB\-p\fR is set, this is a pvalue
cutoff, otherwise, it's a qvalue cutoff. DEFAULT: 0.1
.TP
\fB\-\-verbose\fR=\fIVERBOSE\fR
Set verbose level. 0: only show critical message, 1:
show additional warning message, 2: show process
information, 3: show debug messages. DEFAULT:2