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

# getGeneExpression(1)

compute expression of whole genes

## NAME

getGeneExpression - compute expression of whole genes

## SYNOPSIS

**getGeneExpression** *-o \<outFileName\> -t \<trInfoFileName\>*  \[*OPTIONS*\] \[*samplesFile*\]

## DESCRIPTION

Computes expression of whole genes.

-

  \[samplesFile\] should contain transposed MCMC samples which will be transformed into gene expression samples.

## OPTIONS

**--help**

-

  Show this help information.

**-a** ,   **--adjustByLength**

-

  Adjust expression by transcripts length. (default: Off)

**-g** \<geneInfoFile\> ,   **--geneInfoFile=**\<geneInfoFile\>

-

  Name of while to which gene information will be saved.

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

-

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

**-l** ,   **--log**

-

  Output logged values. (default: Off)

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

-

  Name of the output file.

**--theta2rpkm**

-

  Transform transcript expression in theta to gene expression in RPKM. (default: Off)

**-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)