Altering fastq sequence identifier

Question

[fiona.newberry]

I am attempting to determine false positive/negative of various alignments and want to add a unique sequence identifier onto each fastq file.

I have ten genomes which I have synthetically sequenced (so 20 fq files). The current sequence identifiers look like this:

@simulated.2618103/1

I want to change it so that it looks like this

@simulated.2618103/1.1

Each of the ten genomes will have a sequence identified 1-10. I have tried reading about how to do this with awk but don't seem to understand the program.

Thanks

[venu]

This would help, try to extend the answer in these links

• How do I use sed to remove decimal numbers from a string?

• remove everything after decimal point

• How to delete everything after a certain pattern or a string in a file?

• Replace string after last dot in bash

Answer 1

[GouthamAtla]

Its a bit tricky with fastq as you need to alter only the 1st line of every record ( each record is represented in 4 lines )

So, what you can do is :

awk '{ if (NR%4==1) gsub("$",".1",$1); print }' in.fq > renamed_in.fq

Change the gsub() according to your needs,

[fiona.newberry]

THANK YOU!

do you mind explaining the parts of your awk script? I am really struggling to learn this. Do you know of any good learning material?

[GouthamAtla]

You can read any basic awk tutorials to understand the awk syntax and inbuilt variables.