Extracting only the sequence from fastq files

Question

[padma18krishna]

How to extract only the nucleotide sequence from the entire fastq file containing 1000's of reads using Linux ?

[venu]

Adding to the below answer, this linux tutorial would help you for future tasks.

[GenoMax]

Since a couple of answers below have asked "why anyone would want to do this" I will offer one explanation. It may not be the one applicable in this case.
I remember doing this for someone who wanted to get counts and sequences of all unique combinations present in the dataset. Just counts.

[Ram]

The thing is, it looks like an assignment offloading.

Answer 1

[5heikki]

For example:

paste - - - - <file.fq | cut -f2 > only_seq

Don't know why anyone would want to do that but it's what you asked..

[andrew.j.skelton73]

Agreed, to tack onto this, think about the problem, remember "just because you can, doesn't mean you should..."

Answer 2

[Devon Ryan]

awk '{if(NR%4==2) print $0}' file.fq > seq.txt

No clue why you'd want to do that, but there you go.

[Pierre Lindenbaum]

or just awk '(NR%4==2)' file.fq > seq.txt :-P