NAME

       estimateExpression  -  estimate  expression  given precomputed probabilities of (observed)
       reads alignments

SYNOPSIS

       estimateExpression -o <outFilePrefix>  [OPTIONS] [prob file]

DESCRIPTION

       Estimates expression given precomputed probabilities of (observed) reads' alignments.

              Uses MCMC sampling algorithm to produce relative abundance or RPKM.

OPTIONS

       --help

              Show this help information.

       --MCMC_burnIn=<MCMC_burnIn>

              Length of sampler's burn in period. (default: 1000)

       --MCMC_chainsN=<MCMC_chainsN>

              Number of parallel chains used. At least two chains will be used. (default: 4)

       --MCMC_dirAlpha=<MCMC_dirAlpha>

              Alpha parameter for the Dirichlet distribution. (default: 1)

       --MCMC_samplesDOmax

              Produce maximum number of samples  (samplesNmax)  in  second  iteration  and  quit.
              (default: Off)

       --MCMC_samplesN=<MCMC_samplesN>

              Initial number of samples produced. Doubles after every iteration. (default: 1000)

       --MCMC_samplesNmax=<MCMC_samplesNmax>

              Maximum  number  of  samples produced in one iteration. After producing samplesNmax
              samples sampler finishes. (default: 50000)

       --MCMC_samplesSave=<MCMC_samplesSave>

              Number of samples recorder in total. (default: 1000)

       --MCMC_scaleReduction=<MCMC_scaleReduction>

              Target scale reduction, sampler finishes after this value is met. (default: 1.2)

       -G ,   --gibbs

              Use Gibbs sampling instead of collapsed Gibbs sampling. (default: Off)

       -o <outFilePrefix> ,   --outPrefix=<outFilePrefix>

              Prefix for the output files.

       -O <outputType> ,   --outType=<outputType>

              Output type (theta, RPKM, counts, tau). (default: theta)

       -p <parFileName> ,   --parFile=<parFileName>

              File containing parameters for the sampler, which can  be  otherwise  specified  by
              --MCMC*  options. As the file is checked after every MCMC iteration, the parameters
              can be adjusted while running.

       -P <procN> ,   --procN=<procN>

              Limit the maximum number of threads to be used. (Default  is  the  number  of  MCMC
              chains.)

       --scaleReduction

              Use  scale  reduction  as stopping criterion, instead of computing effective sample
              size. (default: Off)

       -s <seed> ,   --seed=<seed>

              Random initialization seed.

       --thetaActFile=<thetaActFileName>

              File for logging noise parameter theta^{act}.

       -t <trInfoFileName> ,   --trInfoFile=<trInfoFileName>

              File containing transcript information. (Necessary for RPKM)

       -v ,   --verbose

              Verbose output. (default: Off)