star_genome_index: Index genome for STAR alignment

View source: R/04_read_mapping.R

star_genome_indexR Documentation

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/gead documentation built on April 26, 2023, 3:47 p.m.