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Extracting only the sequence from fastq files

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

fastq linux
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updated by Devon Ryan Devon Ryan • written by padma18krishna • padma18krishna

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

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written by venu venu

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.

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written by GenoMax GenoMax

The thing is, it looks like an assignment offloading.

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written by Ram Ram

2 answers

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..

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written by 5heikki 5heikki

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

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written by andrew.j.skelton73 andrew.j.skelton73

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

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

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written by Devon Ryan Devon Ryan

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