Provided by: macs_2.2.9.1-1_amd64 bug

NAME

       macs2_callpeak - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs2 callpeak [-h] -t TFILE [TFILE ...] [-c [CFILE ...]]

       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
              [-g  GSIZE] [-s TSIZE] [--keep-dup KEEPDUPLICATES] [--outdir OUTDIR] [-n NAME] [-B]
              [--verbose VERBOSE] [--trackline] [--SPMR] [--nomodel] [--shift  SHIFT]  [--extsize
              EXTSIZE] [--bw BW] [--d-min D_MIN] [-m MFOLD MFOLD] [--fix-bimodal] [-q QVALUE | -p
              PVALUE]  [--scale-to  {large,small}]  [--down-sample]  [--seed   SEED]   [--tempdir
              TEMPDIR]   [--nolambda]  [--slocal  SMALLLOCAL]  [--llocal  LARGELOCAL]  [--max-gap
              MAXGAP]    [--min-length    MINLEN]    [--broad]    [--broad-cutoff    BROADCUTOFF]
              [--cutoff-analysis]    [--call-summits]   [--fe-cutoff   FECUTOFF]   [--buffer-size
              BUFFER_SIZE] [--to-large] [--ratio RATIO]

   options:
       -h, --help
              show this help message and exit

   Input files arguments:
       -t TFILE [TFILE ...], --treatment TFILE [TFILE ...]
              ChIP-seq treatment file. If multiple files are given as '-t A B C', then they  will
              all be read and pooled together. REQUIRED.

       -c [CFILE ...], --control [CFILE ...]
              Control  file.  If  multiple  files are given as '-c A B C', they will be pooled to
              estimate ChIP-seq background noise.

       -f      {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE},       --format
       {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}
              Format  of  tag  file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or
              "SAM" or "BAM" or "BOWTIE" or "BAMPE" or "BEDPE". The default AUTO option will  let
              MACS  decide  which  format  (except for BAMPE and BEDPE which should be implicitly
              set) the file is. Please check the definition in README. Please note  that  if  the
              format  is  set  as  BAMPE or BEDPE, MACS2 will call its special Paired-end mode to
              call peaks by piling up the actual ChIPed fragments defined by both  aligned  ends,
              instead of predicting the fragment size first and extending reads. Also please note
              that the BEDPE only contains three columns, and is NOT the same BEDPE  format  used
              by BEDTOOLS.  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/read  length. This will override the auto detected tag size. DEFAULT: Not
              set

       --keep-dup KEEPDUPLICATES
              It controls the behavior towards duplicate tags at the exact same location  --  the
              same  coordination  and the same strand. The '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. Note,  if  you've  used
              samtools or picard to flag reads as 'PCR/Optical duplicate' in bit 1024, MACS2 will
              still read them although the reads may be decided by MACS2 as duplicate  later.  If
              you  plan  to  rely  on samtools/picard/any other tool to filter duplicates, please
              remove those duplicate reads and save a new alignment file then ask MACS2  to  keep
              all  by  '--keep-dup  all'.  The  default  is to keep one tag at the same location.
              Default: 1

   Output arguments:
       --outdir OUTDIR
              If specified all output files will be  written  to  that  directory.  Default:  the
              current working directory

       -n NAME, --name NAME
              Experiment name, which will be used to generate output file names. DEFAULT: "NA"

       -B, --bdg
              Whether  or  not  to  save  extended  fragment pileup, and local lambda tracks (two
              files) at every bp into a bedGraph file. DEFAULT: False

       --verbose VERBOSE
              Set verbose level of runtime message.  0:  only  show  critical  message,  1:  show
              additional  warning  message,  2: show process information, 3: show debug messages.
              DEFAULT:2

       --trackline
              Tells MACS to include trackline with bedGraph files.   To  include  this  trackline
              while  displaying bedGraph at UCSC genome browser, can show name and description of
              the file as well. However my suggestion is to convert bedGraph to bigWig, then show
              the  smaller  and  faster  binary  bigWig  file  at UCSC genome browser, as well as
              downstream analysis. Require -B to be set. Default: Not include trackline.

       --SPMR If True, MACS will SAVE signal per million reads for fragment pileup  profiles.  It
              won't  interfere with computing pvalue/qvalue during peak calling, since internally
              MACS2 keeps using the raw pileup and scaling factors  between  larger  and  smaller
              dataset  to calculate statistics measurements. If you plan to use the signal output
              in bedGraph to call peaks using bdgcmp and  bdgpeakcall,  you  shouldn't  use  this
              option  because  you  will  end up with different results.  However, this option is
              recommended for displaying normalized pileup tracks across many  datasets.  Require
              -B to be set. Default: False

   Shifting model arguments:
       --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 extsize to change it.  It's highly
              recommended  that  while  you have many datasets to process and you plan to compare
              different conditions, aka differential calling, use both 'nomodel' and 'extsize' to
              make signal files from different datasets comparable. DEFAULT: False

       --shift SHIFT
              (NOT  the  legacy  --shiftsize  option!)  The arbitrary shift in bp. Use discretion
              while setting it other than default value. When NOMODEL is set, MACS will use  this
              value  to  move  cutting  ends  (5') towards 5'->3' direction then apply EXTSIZE to
              extend them to fragments. When this value is negative, ends will  be  moved  toward
              3'->5'  direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1
              * half of EXTSIZE together with EXTSIZE option for detecting enriched cutting  loci
              such  as  certain  DNAseI-Seq  datasets. Note, you can't set values other than 0 if
              format is BAMPE or BEDPE for paired-end data. DEFAULT: 0.

       --extsize EXTSIZE
              The arbitrary extension size in bp. When nomodel is true, MACS will use this  value
              as  fragment  size  to  extend  each  read towards 3' end, then pile them up.  It's
              exactly twice the number of obsolete SHIFTSIZE.  In previous language, each read is
              moved  5'->3'  direction  to  middle  of  fragment  by 1/2 d, then extended to both
              direction with 1/2 d. This is equivalent to  say  each  read  is  extended  towards
              5'->3' into a d size fragment. DEFAULT: 200. EXTSIZE and SHIFT can be combined when
              necessary. Check SHIFT option.

       --bw BW
              Band width for picking regions to compute fragment size. This value  is  only  used
              while building the shifting model. Tweaking this is not recommended.  DEFAULT: 300

       --d-min D_MIN
              Minimum  fragment size in basepair. Any predicted fragment size less than this will
              be excluded.  DEFAULT: 20

       -m MFOLD MFOLD, --mfold MFOLD MFOLD
              Select the regions within MFOLD range of highconfidence  enrichment  ratio  against
              background  to  build  model.  Fold-enrichment  in regions must be lower than upper
              limit, and higher than the lower limit. Use as "-m 10 30".  This  setting  is  only
              used  while  building the shifting model. Tweaking it is not recommended. DEFAULT:5
              50

       --fix-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 --exsize parameter to extend
              each tags towards 3' direction. Not to use this  automate  fixation  is  a  default
              behavior now. DEFAULT: False

   Peak calling arguments:
       -q QVALUE, --qvalue QVALUE
              Minimum  FDR  (q-value)  cutoff  for peak detection.  DEFAULT: 0.05. -q, and -p are
              mutually exclusive.

       -p PVALUE, --pvalue PVALUE
              Pvalue cutoff for peak detection. DEFAULT:  not  set.   -q,  and  -p  are  mutually
              exclusive.  If  pvalue cutoff is set, qvalue will not be calculated and reported as
              -1 in the final .xls file.

       --scale-to {large,small}
              When set to 'small', scale the larger sample up to the smaller sample. When set  to
              'larger',  scale  the  smaller sample up to the bigger sample. By default, scale to
              'small'. This option replaces  the  obsolete  '  --to-large'  option.  The  default
              behavior  is  recommended  since  it  will  lead  to less significant p/q-values in
              general but more specific results. Keep in mind that scaling  down  will  influence
              control/input  sample  more.  DEFAULT:  'small',  the  choice  is either 'small' or
              'large'.

       --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.  <not  implmented>If  used  together  with --SPMR, 1
              million unique reads will be randomly picked.</not implemented> Caution: due to the
              implementation,  the  final  number  of  selected reads may not be as you expected!
              DEFAULT: False

       --seed SEED
              Set the random seed while down sampling data. Must be  a  non-negative  integer  in
              order to be effective.  DEFAULT: not set

       --tempdir TEMPDIR
              Optional directory to store temp files. DEFAULT: /tmp

       --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 the potential chromatin accessibility.

       --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 while  the  control  data  is
              available.  The  final  local bias would be the maximum of the lambda value from d,
              slocal, and llocal size windows. While control  is  not  available,  d  and  slocal
              lambda won't be considered. 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
              while the control data is available. The final local bias would be the  maximum  of
              the  lambda  value  from  d,  slocal, and llocal size windows. While control is not
              available, d and slocal lambda won't be considered. DEFAULT: 10000.

       --max-gap MAXGAP
              Maximum gap between significant sites to cluster them together. The  DEFAULT  value
              is the detected read length/tag size.

       --min-length MINLEN
              Minimum length of a peak. The DEFAULT value is the predicted fragment size d. Note,
              if you set a value smaller than the fragment size, it may have  NO  effect  on  the
              result.  For  BROAD  peak calling, try to set a large value such as 500bps. You can
              also use '-- cutoff-analysis' option with default setting,  and  check  the  column
              'avelpeak' under different cutoff values to decide a reasonable minlen value.

       --broad
              If  set, MACS will try to call broad peaks using the --broad-cutoff setting. Please
              tweak '--broad-cutoff' setting  to  control  the  peak  calling  behavior.  At  the
              meantime,  either  -q  or  -p  cutoff will be used to define regions with 'stronger
              enrichment' inside of broad peaks. The maximum  gap  is  expanded  to  4  *  MAXGAP
              (--max-gap  parameter).  As  a  result,  MACS  will  output  a  'gappedPeak'  and a
              'broadPeak' file instead of 'narrowPeak' file. Note, a broad peak will be  reported
              even if there is no 'stronger enrichment' inside.  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. Please note  that
              in  broad  peakcalling  mode,  MACS2  uses this setting to control the overall peak
              calling behavior, then uses -q or -p setting to define regions inside broad  region
              as 'stronger' enrichment. DEFAULT: 0.1

       --cutoff-analysis
              While set, MACS2 will analyze number or total length of peaks that can be called by
              different p-value cutoff then output a summary table to help user decide  a  better
              cutoff.  The table will be saved in NAME_cutoff_analysis.txt file. Note, minlen and
              maxgap may affect the results. WARNING: May take ~30 folds longer time  to  finish.
              The  result  can  be useful for users to decide a reasonable cutoff value. DEFAULT:
              False

   Post-processing options:
       --call-summits
              If set, MACS will use a more  sophisticated  signal  processing  approach  to  find
              subpeak summits in each enriched peak region. DEFAULT: False

       --fe-cutoff FECUTOFF
              When  set,  the  value  will  be used to filter out peaks with low fold-enrichment.
              Note, MACS2 use 1.0 as pseudocount while calculating fold-enrichment.  DEFAULT: 1.0

   Other options:
       --buffer-size BUFFER_SIZE
              Buffer size for  incrementally  increasing  internal  array  size  to  store  reads
              alignment  information.  In  most  cases,  you don't have to change this parameter.
              However, if  there  are  large  number  of  chromosomes/contigs/scaffolds  in  your
              alignment,  it's  recommended to specify a smaller buffer size in order to decrease
              memory usage (but it will take longer time to read alignment files). Minimum memory
              requested  for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8
              Bytes. DEFAULT: 100000

   Obsolete options:
       --to-large
              Obsolete option. Please use '--scale-to large' instead.

       --ratio RATIO
              Obsolete option. Originally  designed  to  normalize  treatment  and  control  with
              customized ratio, now it won't have any effect.