Provided by: macs_2.0.9.1-1_amd64 
NAME
macs2diff - Differential Analysis for ChIP-Sequencing
SYNOPSIS
macs2diff <-t1 tfile1> [-c1 cfile1] <-t2 tfile2> [-c2 cfile2] [-n name] [-g genomesize] [options]
DESCRIPTION
Example: macs2diff --t1 CTCF_GM12878.bam --c1 Control_GM12878.bam --t2 CTCF_K562.bam --c2
Control_K562.bam -g hs -n testdiff -B -q 0.01
macs2diff -- Differential Analysis for ChIP-Sequencing
OPTIONS
--version
show program's version number and exit
-h, --help
show this help message and exit.
--t1=TFILE1
ChIP-seq treatment file for the first condition. REQUIRED.
--c1=CFILE1
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.
--t2=TFILE2
ChIP-seq treatment file for the second condition. REQUIRED
--c2=CFILE2
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.
-n NAME, --name=NAME
Analysis 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
-B, --bdg
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
--minlen=MINLEN
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.
-a NPROCESSES
Number of CPUs MACS can use, upto 4. DEFAULT: 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