kallistoIndex: Builds a transcriptome index (.idx) from a FASTA-formatted...

In nixstix/RNASeqAnalysis: Analysis of RNA-Seq data: QC filtering, expression analysis, differential expression pipeline

Description

kallistoIndex builds an index of the transcriptome. Once built, the transcriptome index (in the form of a De Bruijn graph) may be used for pseudoalignment of the target RNA-Seq data in order to quantify expression (see kallistoQuant). A transcriptome De Bruijn graph (T-DBG) is constructed from k-mers in the transcriptome, where each k-mer in the transcriptome is a node in the T-DBG. Each transcript is represented by a different colour, and whenever a node appears in a transcript, it is given the colour of that transcript. MORE. Kallisto must be installed locally. Kallisto can be downloaded from https://pachterlab.github.io/kallisto/download.html.

Usage

kallistoIndex(refTranscriptome, indexName = "./transcripts.idx")

Arguments

refTranscriptome	A character string of the transcriptome file (in fasta format) to be indexed.
indexName	A character string of the output index file to be created. Default is "./transcripts.idx").

Value

An index file (.idx) which can be used to quantify expression data using kallistoQuant pseudoalignment.

See Also

http://pachterlab.github.io/kallisto/ for more about Kallisto.

Examples

kallistoIndex("./transcripts.fasta")
kallistoIndex("./transcripts.fa.gz", "./index.idx")
 

nixstix/RNASeqAnalysis documentation built on May 23, 2019, 7:06 p.m.