NAME

       mac3_bdgcmp - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs3 bdgcmp [-h] -t TFILE -c CFILE [-S SFACTOR] [-p PSEUDOCOUNT]

       [-m {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max}
       ...]]
              [--verbose VERBOSE] [--outdir OUTDIR] (--o-prefix OPREFIX | -o OFILE [OFILE ...])

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

       -t, --tfile TFILE
              Treatment bedGraph file, e.g. *_treat_pileup.bdg from MACSv2. REQUIRED

       -c, --cfile CFILE
              Control bedGraph file, e.g. *_control_lambda.bdg from MACSv2. REQUIRED

       -S, --scaling-factor SFACTOR
              Scaling  factor  for  treatment and control track. Keep it as 1.0 or default in most cases. Set it
              ONLY while you have SPMR output from MACS3  callpeak,  and  plan  to  calculate  scores  as  MACS3
              callpeak  module. If you want to simulate 'callpeak' w/o '--to-large', calculate effective smaller
              sample size after filtering redudant reads in million (e.g., put 31.415926 if effective reads  are
              31,415,926)  and input it for '-S'; for 'callpeak --to-large', calculate effective reads in larger
              sample. DEFAULT: 1.0

       -p, --pseudocount PSEUDOCOUNT
              The pseudocount used for calculating  logLR,  logFE  or  FE.  The  count  will  be  applied  after
              normalization of sequencing depth. DEFAULT: 0.0, no pseudocount is applied.

       -m, --method {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max}
       [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} ...]
              Method to use while calculating a score in any bin by comparing treatment value and control value.
              Available  choices  are: ppois, qpois, subtract, logFE, FE, logLR, slogLR, and max. They represent
              Poisson Pvalue (-log10(pvalue) form) using control as lambda and treatment as observation, q-value
              through a  BH  process  for  poisson  pvalues,  subtraction  from  treatment,  linear  scale  fold
              enrichment, log10 fold enrichment(need to set pseudocount), log10 likelihood between ChIP-enriched
              model  and  open  chromatin model(need to set pseudocount), symmetric log10 likelihood between two
              ChIP-enrichment models, or maximum value between the two tracks. Default option is ppois.

       --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

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

       --o-prefix OPREFIX
              The PREFIX of output bedGraph file to write scores. If it is given as A, and  method  is  'ppois',
              output file will be A_ppois.bdg. Mutually exclusive with -o/--ofile.

       -o, --ofile OFILE [OFILE ...]
              Output  filename.  Mutually  exclusive with --o-prefix.  The number and the order of arguments for
              --ofile must be the same as for -m.

macs3 bdgcmp 3.0.2                                 March 2025                                     MAC3_BDGCMP(1)