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

# parseAlignment(1)

pre-compute probabilities of (observed) reads alignments

## NAME

parseAlignment - pre-compute probabilities of (observed) reads alignments

## SYNOPSIS

**parseAlignment** *-o \<outFileName\> -s \<trSeqFileName\>*  \[*OPTIONS*\] \[*alignment file*\]

## DESCRIPTION

Pre-computes probabilities of (observed) reads' alignments.

-

  \[alignment file\] should be in either SAM or BAM format.

## OPTIONS

**--help**

-

  Show this help information.

**--distributionFile=**\<distributionFileName\>

-

  Name of file to which read-distribution should be saved.

**--excludeSingletons**

-

  Exclude single mate alignments for paired-end reads. (default: Off)

**-e** \<expFileName\> ,   **--expressionFile=**\<expFileName\>

-

  Transcript relative expression estimates **---** for better non-uniform read distribution estimation.

**--failed=**\<failed\>

-

  File name where to save names of reads that failed to align.

**-f** \<format\> ,   **--format=**\<format\>

-

  Input format: either SAM, BAM.

**--lenMu=**\<lenMu\>

-

  Set mean of log fragment length distribution. (l\_frag ~ LogNormal(mu,sigma^2))

**--lenSigma=**\<lenSigma\>

-

  Set sigma^2 (or variance) of log fragment length distribution. (l\_frag ~ LogNormal(mu,sigma^2))

**--mateNamesDiffer**

-

  Mates from paired-end reads have different names. (default: Off)

**-l** \<maxAlignments\> ,   **--limitA=**\<maxAlignments\>

-

  Limit maximum number of alignments per read. (Reads with more alignments are skipped.)

**--noiseMismatches=**\<numNoiseMismatches\>

-

  Number of mismatches to be considered as noise. (default: 6)

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

-

  Name of the output file.

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

-

  Maximum number of threads to be used. This provides speedup mostly when using non-uniform read distribution model (i.e. no **--uniform** flag). (default: 4)

**-N** \<readsN\> ,   **--readsN=**\<readsN\>

-

  Total number of reads. This is not necessary if \[SB\]AM contains also reads with no valid alignments.

**--show1warning**

-

  Show first alignments that are considered wrong (TID unknown, TID mismatch, wrong strand). (default: Off)

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

-

  File to save transcript information extracted from \[BS\]AM file and reference.

**-s** \<trSeqFileName\> ,   **--trSeqFile=**\<trSeqFileName\>

-

  Transcript sequence in FASTA format **---** for non-uniform read distribution estimation.

**--trSeqHeader=**\<trSeqHeader\>

-

  Transcript sequence header format enables gene name extraction (standard/gencode). (default: standard)

**--uniform**

-

  Use uniform read distribution. (default: Off)

**--unstranded**

-

  Paired read are not strand specific. (default: Off)

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

-

  Verbose output. (default: Off)

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

-

  Very verbose output. (default: Off)