notepad++ text edit, fastq

Question

[Rob]

strong textHi friends, I have a fastq file and I want to remove characters in the lines started with + and replace it with only "+" I tried in text editor but I couldn't as the number of characters are different in the lines with +.

Do you have any suggestion that helps me with this?

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[Pierre Lindenbaum]

[Carlo Yague]

Why would you want to do that ?

[Rob]

it is a question for my class and I have to be able to do it in notepad++ or excel

[ATpoint]

Then tell whoever is giving this class they they have no clue what they're doing when forcing students to manipulate omics data by hand. That is plain terrible. Opening fastq files in Excel, dear lord...

[Rob]

Lol yeah it really sucks and took lots of my time and effort anyways I have to do that for this class and will leave and forget it forever after this class

[Dunois]

May I ask who is teaching this class and/or where it's being taught?

[cpad0112]

$ sed -r '3~4 s/^.*$/+/' test.fq

[GenoMax]

Aside from reasons of why this should not be done that have been mentioned, this could simply be a question about using a regular expression to make this change. NotePad++ is supposed to be able to use regular expression in search/replacements.

[Rob]

yes it is for using regex

[GenoMax]

yes it is for using regex

You left out that critical piece of information in your original question. Using NotePad++ was your idea or was that a requirement (seems unlikely but one never knows).

[Rob]

hi it is the requirement to use notepad++ for this part

Answer 1

[ATpoint]

Never edit raw data by hand. This is both error-prone, irreproducible and for larger files not possible.

paste - - - -  < foo.fq | awk 'OFS="\n" {print $1, $2, "+", $4}'