star_align: Align reads to a reference genome using STAR

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

Align reads to a reference genome using STAR

Description

Align reads to a reference genome using STAR

Usage

star_align(
  sample_info = NULL,
  filtdir = "results/03_filtered_FASTQ",
  qc_table = NULL,
  mappingdir = "results/04_read_mapping",
  gff_path = NULL,
  threads = 1
)

Arguments

sample_info	Data frame of sample metadata created with the function create_sample_info.
filtdir	Path to the directory where filtered reads will be stored. Default: results/03_filtered_FASTQ.
qc_table	Data frame of fastp summary statistics as returned by summary_stats_fastp().
mappingdir	Path to the directory where read mapping files (.bam) will be stored.
gff_path	Path to the .gff/.gtf file with annotations.
threads	Number of threads for STAR aligner. Default: 1.

Value

A 2-column data frame with BioSample IDs in the first column and STAR running status in the second column, with "OK" if reads were mapped (.bam files were created) and NA if STAR failed to map reads.

Examples

data(sample_info)
qc_table <- summary_stats_fastp(system.file("extdata", package = "bears"))
genome_path <- system.file("extdata", "Hsapiens_GRCh37.75_subset.fa", 
                            package="bears")
gff_path <- system.file("extdata", "Homo_sapiens.GRCh37.75_subset.gtf", 
                         package="bears")
mappingdir <- tempdir()
filtdir <- system.file("extdata", package="bears")
if(star_is_installed()) {
    star_genome_index(genome_path, gff_path, mapping_dir, indexdir)
    star_align(sample_info, filtdir, qc_table, mappingdir, gff_path)
}

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