Use RSEM to prepare reference genome

Source: R/prepare_reference_genome.R

use rsem-prepare-reference to generate reference genome for mapping RNAseq transcripts

prepare_reference_genome(parameters, verbose = TRUE)

Arguments

parameters

as read in by load_parameters()
verbose

(default: TRUE)

Details

# Usage example: in parameters.yaml

source_data: genome: transcript_fasta_path: "raw_data/FungiDB-49_CneoformansH99_AnnotatedTranscripts.fasta" data_paths: reference_genome_path: "/scratch/maom_root/maom99/maom/CryptoCEN/reference_genome/CneoformansH99" software_paths: bowtie2_path: "/home/maom/opt/bowtie2-2.3.4.1-linux-x86_64" fastq_dump_program: "/home/maom/opt/bin/fastq-dump" rsem_path: "/home/maom/opt/RSEM/"

In R:

library(CalCEN) parameters <- CalCEN::load_parameters() CalCEN::prepare_reference_genome()