buildGenomeIndexSTAR: Build a genome index for STAR

In RGLab/RNASeqPipelineR: Construct Standardized pipelines for processing RNASeq data

Description

Builds a genome Index at 'Utils/Reference_Genome/STARIndex'

Usage

buildGenomeIndexSTAR(path = NULL, gtf_file = "", fasta_file = NULL,
  star_threads = 1, name = NULL)

Arguments

path	character specifying an absolute path path to the Utils directory.
gtf_file	character the name of the gtf file.
fasta_file	character the name of the fasta file, must be specified
star_threads	integer specify how many threads star should use.
name	character the name of the genome output

Details

You must specify the Utils path if it is not already defined, and have your genome and annotation file in a folder titled 'Reference_Genome'. This function will construct the genome index using STAR tools. The command line is the default shown in the documentation. A fasta_file must be provided. gtf_file is highly recommended, and if not provided, STAR will run without annotations.

RGLab/RNASeqPipelineR documentation built on Jan. 19, 2020, 12:31 a.m.