---
name: "getWithinGeneExpression"
section: "1"
platform: "linux"
package: "bitseq"
version: "0.7.5+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/getWithinGeneExpression"
---

# getWithinGeneExpression(1)

compute relative expression of transcripts within genes

## 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)