NAME

       macs2_bdgcmp - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs2 bdgcmp [-h] -t TFILE -c CFILE [-S SFACTOR] [-p PSEUDOCOUNT]

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

   optional arguments:
       -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 MACS2 callpeak, and plan to
              calculate scores as MACS2 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}
       [{ppois,qpois,subtract,logFE,FE,logLR,slogLR}                ...],                --method
       {ppois,qpois,subtract,logFE,FE,logLR,slogLR} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR}
       ...]
              Method to use while calculating a score in any bin by comparing treatment value and
              control  value.  Available  choices  are: ppois, qpois, subtract, logFE, logLR, and
              slogLR. 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), and symmetric  log10  likelihood
              between two ChIP-enrichment models. Default option is ppois.

       --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.