parseAlignment: Compute probabilities of alignments

In BitSeq: Transcript expression inference and differential expression analysis for RNA-seq data

Description

Compute probability of alignments and save them into .prob file.

Usage

parseAlignment( alignFile, outFile, trSeqFile, inputFormat=NULL, trInfoFile=NULL, 
      expressionFile=NULL, readsN=NULL, uniform=TRUE, limitA=NULL, lenMu=NULL,
      lenSigma=NULL, excludeSingletons=NULL, mateNamesDiffer=NULL,
      verbose=NULL, veryVerbose=NULL, procN=NULL, pretend=FALSE)

Arguments

alignFile	File containing read alignments.
outFile	Name of the output file.
inputFormat	Input format: possible values SAM, BAM. (This should be detected automatically in most cases.)
trInfoFile	File to save transcript information extracted from [BS]AM file and reference.
trSeqFile	File containing transcript sequence in FASTA format.
expressionFile	Transcript relative expression estimates — for better non-uniform read distribution estimation.
readsN	Total number of reads. This is usually not necessary if SAM/BAM contains also reads with no valid alignments.

uniform	Use uniform read distribution.
limitA	Limit maximum number of alignments per read. Reads with more alignments than limit will be discarded.
lenMu	Set mean of log fragment length distribution. l_frag ~ LogNormal(mu,sigma^2)
lenSigma	Set sigma^2 (or variance) of log fragment length distribution. l_frag ~ LogNormal(mu,sigma^2)

excludeSingletons	Exclude single mate alignments for paired-end reads.
mateNamesDiffer	Mates from paired-end reads have different names.
verbose	Verbose output.
veryVerbose	Very verbose output.
procN	Maximum number of threads to be used.
pretend	Do not execute, only print out command line calls for the C++ version of the program.

Details

This function uses the alignments and reference file to assign probability to each alignment. It uses either bias-corrected or uniform model for the read distribution, assumes Log-Normal distribution of fragment lengths for pair-end read data and uses quality scores and mismatches to assign probability for every alignment of a read (or fragment) to a transcript.

Value

.prob	file containing the alignment probabilities
.tr	file containing reference transcript names, lengths and effective lengths - optional

Author(s)

Peter Glaus

See Also

estimateExpression

Examples

## Not run: 
parseAlignment(alignFile="data.sam", outFile="data.prob", 
      trSeqFile="trReference.fa" ,trInfoFile="data.tr")

## End(Not run)

BitSeq documentation built on Nov. 8, 2020, 5:25 p.m.