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

# estimateVBExpression(1)

estimate expression given precomputed probabilities of (observed) reads alignments

## NAME

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

## SYNOPSIS

**estimateVBExpression** *-o \<outFilePrefix\>*  \[*OPTIONS*\] \[*prob file*\]

## DESCRIPTION

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

-

  Uses Variational Bayes algorithm to produce parameters for distribution of relative abundances.

## OPTIONS

**--help**

-

  Show this help information.

**--optLimit=**\<limit\>

-

  Optimisation limit in terms of minimal gradient or change of bound. (default: 1e-05)

**--maxIter=**\<maxIter\>

-

  Maximum number of iterations. (default: 10000)

**-m** \<optMethod\> ,   **--method=**\<optMethod\>

-

  Optimization method (steepest, PR, FR, HS). (default: FR)

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

-

  Prefix for the output files.

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

-

  Output type (theta, RPKM, counts) of the samples sampled from the distribution. (default: theta)

**-P** \<procN\> ,   **--procN=**\<procN\>

-

  Limit the maximum number of threads to be used. (default: 4)

**--samples=**\<samples\>

-

  Number of samples to be sampled from the distribution.

**-s** \<seed\> ,   **--seed=**\<seed\>

-

  Random initialization seed.

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

-

  File containing transcript information. (Necessary for RPKM samples)

**-v** ,   **--verbose**

-

  Verbose output. (default: Off)

**-V** ,   **--veryVerbose**

-

  More verbose output, better if output forwarded into file. (default: Off)