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Altering fastq sequence identifier

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

fastq
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updated by GouthamAtla GouthamAtla • written by fiona.newberry fiona.newberry

1 answer

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,

• 0 views • link
written by GouthamAtla GouthamAtla

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?

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written by fiona.newberry fiona.newberry

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

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written by GouthamAtla GouthamAtla

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