read_fastq: Read in raw data from a fastq file.

In debar: A Post-Clustering Denoiser for COI-5P Barcode Data

Read in raw data from a fastq file.

Description

Read in raw data from a fastq file.

Usage

read_fastq(x, keep_quality = TRUE)

Arguments

x	The name of the fastq file to read data from.
keep_quality	Boolean indicating if the Phred quality scores should be retained in the output dataframe. Default is TRUE.

Examples

#read in an unzipped fastq file
fastq_example_file = system.file('extdata/coi_sequel_data_subset.fastq', 
                                  package = 'debar')
data = read_fastq(fastq_example_file)
#read in a gzipped fastq file and do not keep the phred scores
gz_fastq_example_file = system.file('extdata/coi_sequel_data_subset.fastq', 
                                    package = 'debar')
data2 = read_fastq(gz_fastq_example_file, keep_quality = FALSE)

debar documentation built on May 29, 2024, 2:02 a.m.