Remove rRNA sequences from .fastq files with SortMeRNA
Usage
remove_rrna(
sample_info,
fastqdir = "results/01_FASTQ_files",
filtdir = "results/03_filtered_FASTQ",
rrna_db_dir = NULL,
threads = 1
)
Arguments
- sample_info
Data frame of sample metadata created with the function
create_sample_info
.- fastqdir
Path to the directory where .fastq files are stored.
- filtdir
Path to the directory where filtered reads will be stored. Default: results/03_filtered_FASTQ.
- rrna_db_dir
Path to directory containing reference rRNA database, which must be stored as FASTA files.
- threads
Number of threads for SortMeRna. Default: 1.
Value
A 2-column data frame with run accessions in the first column and SortMeRNA running status in the second column, with "OK" if SortMeRNA ran successfully for each file and NA otherwise.
Examples
data(sample_info)
fastqdir <- system.file("extdata", package="bears")
filtdir <- tempdir()
rrna_db_dir <- tempdir()
rrna_file <- system.file("extdata", "bac_16s_subset.fa", package="bears")
file.copy(from = rrna_file, to = rrna_db_dir)
#> [1] TRUE
if(sortmerna_is_installed()) {
remove_rrna(sample_info, fastqdir, filtdir, rrna_db_dir)
}