star_genome_index: Index genome for STAR alignment

In almeidasilvaf/GEAtlas: Building Expression Atlas from RNA-Seq data

Index genome for STAR alignment

Description

Index genome for STAR alignment

Usage

star_genome_index(
  genome_path = NULL,
  gff_path = NULL,
  mappingdir = "results/04_read_mapping",
  threads = 2
)

Arguments

genome_path	Path to the genome .fasta file.
gff_path	Path to the .gff/.gtf file with annotations.
mappingdir	Path to the directory where read mapping files (.bam) will be stored.
threads	Number of threads for STAR aligner. Default: 2.

Value

A 2-column data frame with path to index in the first column and index build status in the second column, with "OK" if the index was built successfully and NA otherwise.

Examples

genome_path <- system.file("extdata", "Homo_sapiens.GRCh37.75_subset.fa", 
                            package="bears")
gff_path <- system.file("extdata", "Homo_sapiens.GRCh37.75_subset.gtf", 
                         package="bears")
mappingdir <- tempdir()
if(star_is_installed()) {
    star_genome_index(genome_path, gff_path, mapping_dir)
}

almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.