Trim low-quality bases and adapters using fastp
Usage
trim_reads(
sample_info = NULL,
fastqdir = "results/01_FASTQ_files",
filtdir = "results/03_filtered_FASTQ",
qcdir = "results/QC_dir/fastp_stats",
threads = 1,
delete_raw = FALSE
)
Arguments
- sample_info
Data frame of sample metadata created with the function
create_sample_info
.- fastqdir
Path to the directory where .fastq files will be stored. Default: results/01_FASTQ_files.
- filtdir
Path to the directory where filtered .fastq files will be temporarily stored. After trimming, filtered reads are moved back to fastqdir. Default: results/03_filtered_FASTQ.
- qcdir
Character indicating the path to the directory where output summary stats will be saved. Default: results/QC_dir/fastp_stats.
- threads
Numeric indicating the number of threads to use in fastp. Default: 1.
- delete_raw
Logical indicating whether to delete raw (unfiltered) FASTQ files after QC and filtering with fastp. It is recommended to delete raw files, as they use much memory and the useful information will be on filtered files, even if no filtering is performed. Default: FALSE.
Value
A 2-column data frame with run accession in the first column and fastp run status in the second column, with "OK" if it ran successfully and NA if a file could not be run.
Examples
data(sample_info)
fastqdir <- tempdir()
file.copy(system.file("extdata", "SRR1039508_1.fastq.gz", package = "bears"),
fastqdir)
#> [1] FALSE
file.copy(system.file("extdata", "SRR1039508_2.fastq.gz", package = "bears"),
fastqdir)
#> [1] FALSE
filtdir <- paste0(fastqdir, "/filtdir")
qcdir <- file.path(tempdir(), "qcdir")
if(!dir.exists(filtdir)) { dir.create(filtdir, recursive = TRUE) }
if(!dir.exists(qcdir)) { dir.create(qcdir, recursive = TRUE) }
if(fastp_is_installed()) {
trim_status <- trim_reads(sample_info, fastqdir, filtdir, qcdir)
}