microseq (version 2.1.6)

readFastq: Read and write FASTQ files

Description

Reads and writes files in the FASTQ format.

Usage

readFastq(in.file)
writeFastq(fdta, out.file)

Value

readFastq returns a tibble with the contents of the (gzipped) FASTQ file stored in three columns of text. The first, named Header, contains the headerlines, the second, named Sequence, contains the sequences and the third, named Quality contains the base quality scores.

writeFastq produces a (gzipped) FASTQ file.

Arguments

in.file

url/directory/name of (gzipped) FASTQ file to read.

fdta

FASTQ object to write.

out.file

url/directory/name of (gzipped) FASTQ file to write.

Author

Lars Snipen and Kristian Hovde Liland.

Details

These functions handle input/output of sequences in the commonly used FASTQ format, typically used for storing DNA sequences (reads) after sequencing. If filenames (in.file or out.file) have the extension .gz they will automatically be compressed/uncompressed.

The sequences are stored in a tibble, opening up all the possibilities in R for fast and easy manipulations. The content of the file is stored as three columns, Header, Sequence and Quality. If other columns are added, these will be ignored by writeFastq.

See Also

codereadFasta.

Examples

if (FALSE) {
# We need a FASTQ-file to read, here is one example file:
fq.file <- file.path(file.path(path.package("microseq"),"extdata"),"small.fastq.gz")

# Read and write
fdta <- readFastq(fq.file)
ok <- writeFastq(fdta[1:3,], out.file = "delete_me.fq")

# Make use of dplyr to copy parts of the file to another file
readFastq(fq.file) %>% 
  mutate(Length = str_length(Sequence)) %>% 
  filter(Length > 200) %>% 
  writeFasta(out.file = "long_reads.fa") # writing to FASTA file
}