buildReference: Build a reference genome

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

Description

Builds a reference genome at 'path/Reference_Genome/'

Usage

buildReference(path = NULL, gtf_file = NULL, fasta_file = NULL,
  isoformsFile = NULL, name = NULL, doSTAR = TRUE, starPath = NULL,
  threads = 1)

Arguments

path	character specifying an absolute path path to the Reference_Genome directory.
gtf_file	character the name of the gtf file. Empty by default. If specified the function will look for the named file in the 'path' directory
fasta_file	character the name of the fasta file, must be specified and located in the 'path' directory
isoformsFile	character the name if the known isoforms file (optional). If specified it must be located in the 'path' file.
name	character the prefix of the genome output.
doSTAR	logical logical showing whether to build genome with STAR index.
starPath	character full path to the 'star' executable.
threads	integer number of threads to use

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' or if doSTAR=TRUE 'rsem-prepare-reference –gtf gtf_file –transcript-to-gene-map knownIsoforms.txt –star –star-path starPath 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.