Skip to contents

Write a list of sequences and quality scores to a FASTQ file

Source: R/write_list_to_fastq.R
write.list_to_fastq.Rd

This function takes a list of sequences and quality scores and writes them to a FASTQ file. The name of the list is used as the base name for the output file with the .fastq extension. Each sequence in the list is written to the output file in FASTQ format with the sequence name as the header and the quality scores on the following line.

Usage

write.list_to_fastq(sequence_list)

Arguments

sequence_list

A list of sequences where each element of the list is a named list containing "Sequence" and "QualityScore" elements.

Examples

sequences <- list("ACGT", "ATCG")
quality_scores <- list("IIII", "JJJJ")
sequences_list <- list(seq1=list(Sequence=sequences[[1]], QualityScore=quality_scores[[1]]),
                       seq2=list(Sequence=sequences[[2]], QualityScore=quality_scores[[2]]))
write.list_to_fastq(sequences_list)
#> List sequences_list written to FASTQ file sequences_list.fastq