prepare_reference_genome: Use RSEM to prepare reference genome

In momeara/CalCEN: CalCEN: Estimate Co-Expression Networks

Use RSEM to prepare reference genome

Description

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

Usage

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()

momeara/CalCEN documentation built on Jan. 3, 2023, 7:22 p.m.