getBowtie2TranscriptomeReference: Builds and gets a Bowtie2 reference
In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

View source: R/app-transcriptome-mapping.R

getBowtie2TranscriptomeReference

R Documentation

Builds and gets a Bowtie2 reference

Description

Builds and gets a Bowtie2 reference by returning the file path to it.

Usage

getBowtie2TranscriptomeReference(param)

Arguments

param

a list of parameters:

ezRef@refIndex a character specifying the location of the index that is used in the alignment.
ezRef@refBuildDir a character specifying the directory of the reference build.
ezRef@refFeatureFile the gtf file with the transcript coordinates
ezRef@refFastaFile a character specifying the file path to the fasta file.

Value

Returns a character specifying the file path to the Bowtie2 indexed reference genome.

Author(s)

Rehrauer, Hubert

Schmid, Peter

Examples

ls = list('refBuild' = 'Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Version-2013-03-07')
param = ezParam(userParam = ls)
getBowtie2Reference(param)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.