How to exclude reads from a fastq file, using a list of read names?

Question

[Tash]

I have a fastq file from a sequencing run, and I have a list of read names, which I wish to exclude from the fastq files. I am having some trouble filtering the whole entry based on names only. I have pasted my attempts and rationale below, and any assistance would be much appreciated!

cat names_pc3.txt  
a308dbd5-df59-47f2-a92a-7068ffd0ce8d
353002fa-3d36-4e03-a8c4-b6e983464bf9
697f8ebb-9fa7-487e-ae91-8095bfb9968b
05887f55-8028-4524-8000-71e72de789d0

I can exclude the line containing the read name with grep, however I wish to remove the whole 4 line entry for each read.

To remove the line containing the read name, this works:

grep --no-group-separator -v -f names_pc3.txt PAQ11486_pass_barcode01_52e0f3ff_4295e9c8_0.fastq

To view the entry for the reads I want to exclude, this works:

grep --no-group-separator -A 3 -f names_pc3.txt PAQ11486_pass_barcode01_52e0f3ff_4295e9c8_0.fastq

However, when I try to do both at the same time using the command below, it just prints all entries in the fastq:

grep --no-group-separator -A 3 -v -f names_pc3.txt PAQ11486_pass_barcode01_52e0f3ff_4295e9c8_0.fastq

Would love some help with a different approach or correction to my current approach if possible! Thanks.

Answer 1

[Pierre Lindenbaum]

it doesn't work because the reads you want to exclude are within 3 lines of the negative selection of reads (-A 3 -v).

you could use

cat PAQ11486_pass_barcode01_52e0f3ff_4295e9c8_0.fastq |\
paste - - - - |\
grep -v -F -f names_pc3.txt |\
tr "\t" "\n"

see also : How to remove a list of reads from fastq file? ; How To Extract A Subset Of Reads In Fastq Using An Id List? ; removal of spesific read from fastq file ; ...

[Tash]

Thank you so much Pierre, that worked perfectly! Much appreciated.