trim_reads: Trim low-quality bases and adapters using fastp

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

Trim low-quality bases and adapters using fastp

Description

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)
file.copy(system.file("extdata", "SRR1039508_2.fastq.gz", package = "bears"),
          fastqdir)
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)
}

almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.