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
# \donttest{
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)
}
#> Error in file.path(mappingdir, "genomeIndex"): object 'mapping_dir' not found
# }