buildGenomeIndexSTAR2: Build a reference genome 2

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

Description

Builds a reference genome at 'Utils/Reference_Genome'

Usage

buildGenomeIndexSTAR2(path = NULL, gtf_file = "", fasta_file = NULL,
  star_threads = 1, name = NULL, gff3 = FALSE,
  additional_param = "")

Arguments

path	character specifying an absolute path path to the Utils directory.
gtf_file	character the name of the gtf file. Empty by default. If specified the function will look for a file named 'knownIsoforms.txt'
fasta_file	character the name of the fasta file, must be specified
star_threads	integer number of threads to use when building index
name	character the name of the genome output.
gff3	logical when gtf_file is gff3 format set it to TRUE to add "–sjdbGTFtagExonParentTranscript gene".
additional_param	character default "". Additional parameters to pass.

Details

You must specify the Utils path if it is not already defined, and have your genome in a folder titled 'Reference_Genome'. This function will construct the reference genome using RSEM tools. The command line is the default shown in the documentation. 'rsem-prepare-reference –gtf gtf_file –transcript-to-gene-map knownIsoforms.txt –bowtie2 fasta_file name' If the gtf_file is not give, then the transcript-to-gene-map option is not used either. A fasta_file and a name must be provided.

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