readFastqFile: Read and write FASTQ Files

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Read and write FASTQ Files

Description

Read a FASTQ file into a data frame, or write a data frame to a FASTQ file.

Usage

readFastq(filein, maxReads = NULL, verbose = TRUE)
writeFastq(x, fileout, compress = FALSE, verbose = TRUE)

Arguments

filein	full pathname to one existing, optionally compressed, FASTQ file. Compression and .gz file extension are automatically detected.
fileout	full pathname for newly created, optionally compressed, FASTQ file. Compression and .gz file extension are automatically coordinated.
maxReads	integer count of the maximum number of reads wanted, where NULL means read the entire file.
compress	logical, explicitly compress the created file and adjust filename accordingly.

Value

For readFastq, a data frame, with 3 columns:

READ_ID	the ReadID for each short read
READ_SEQ	the nucleotide sequence of each short read
SCORE	the cryptic ASCII Phred score string for each short read

For writeFastq, the name of the created file.

Note

FASTQ data can get quite large. This routine can easily exceed available memory for large maxReads.

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.