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

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

       -S SFACTOR, --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 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                                        {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max}
       [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max}              ...],              --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 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.