.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.13.
.TH MACS2DIFF "1" "December 2012" "macs2diff 2.0.9.1" "User Commands"
.SH NAME
macs2diff \- Differential Analysis for ChIP-Sequencing
.SH SYNOPSIS
.B macs2diff
\fI<-t1 tfile1> \fR[\fI-c1 cfile1\fR] \fI<-t2 tfile2> \fR[\fI-c2 cfile2\fR] [\fI-n name\fR] [\fI-g genomesize\fR] [\fIoptions\fR]
.SH DESCRIPTION
Example: macs2diff \fB\-\-t1\fR CTCF_GM12878.bam \fB\-\-c1\fR Control_GM12878.bam \fB\-\-t2\fR CTCF_K562.bam \fB\-\-c2\fR Control_K562.bam \fB\-g\fR hs \fB\-n\fR testdiff \fB\-B\fR \fB\-q\fR 0.01
.PP
macs2diff \fB\-\-\fR Differential 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\-\-t1\fR=\fITFILE1\fR
ChIP\-seq treatment file for the first condition.
REQUIRED.
.TP
\fB\-\-c1\fR=\fICFILE1\fR
Control file for the first condition. If c1 is missing
while c2 is specified, t1 will be paired with c2. At
least one of c1 or c2 should be available.
.TP
\fB\-\-t2\fR=\fITFILE2\fR
ChIP\-seq treatment file for the second condition.
REQUIRED
.TP
\fB\-\-c2\fR=\fICFILE2\fR
Control file for the second condition. If c2 is
missing while c1 is specified, t2 will be paired with
c1. At least one of c1 or c2 should be available.
.TP
\fB\-n\fR NAME, \fB\-\-name\fR=\fINAME\fR
Analysis 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\-B\fR, \fB\-\-bdg\fR
Whether or not to save p/qvalue (depending on whether
pvalue or qvalue is used) score tracks at every bp
into a bedGraph file. DEFAULT: False
.TP
\fB\-\-minlen\fR=\fIMINLEN\fR
The minimum length for differential calling. By
default, it will be decided as the middle of fragment
sizes of treatment 1 andtreatment 2. Must be an
integar larger than 0.
.TP
\fB\-a\fR NPROCESSES
Number of CPUs MACS can use, upto 4. DEFAULT: 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