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