bionic (1) getWithinGeneExpression.1.gz

NAME

       getWithinGeneExpression - compute relative expression of transcripts within genes

SYNOPSIS

       getWithinGeneExpression -t <trInfoFileName>  [OPTIONS] [samplesFile]

DESCRIPTION

       Computes relative expression of transcripts within genes.

              [samplesFile]  should  contain  transposed MCMC expression samples.  program can produce means and
              variance and write them  into  [sumFile]  or  individual  MCMC  samples  which  are  written  into
              [outFile].

OPTIONS

       --help

              Show this help information.

       -a ,   --adjustByLength

              Adjust expression by transcripts length. (default: Off)

       -G <geneListFile> ,   --geneList=<geneListFile>

              Name of the file containing list of gene names (one for each transcript).

       --groupByGene

              Group transcripts by genes (this can change the default order of output. (default: Off)

       -l ,   --log

              Use logged values. (default: Off)

       -o <outFileName> ,   --outFile=<outFileName>

              Name of the output file.

       -s <sumFileName> ,   --sumFile=<sumFileName>

              Name  of summarization file where true mean, true variance and relative mean and relative variance
              are saved.

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

              Name of the transcript file.

       -T <trMapFile> ,   --trMap=<trMapFile>

              Name of the file containing transcript to gene mapping.

       --updateTrFile

              Update trInfoFile if new gene names were provided (with trMapFile or geneListFile). (default: Off)

       -v ,   --verbose

              Verbose output. (default: Off)