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

# estimateExpression(1)

estimate expression given precomputed probabilities of (observed) reads alignments

## 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)