Filtering FASTQ Files

Question

[cbrown58]

I am trying to filter paired end reads from a FASTQ file based on ones that match to a specific genome. I want to keep any reads that align to the genome. So far all examples of this I have found are to remove the matches, does anyone have any examples of how I can do the reverse?

Thank you.

Answer 1

[GenoMax]

You can use bbsplit.sh from BBMap suite with the genome of your interest to bin the reads or use bbduk.sh from same suite.

[cbrown58]

Thank you, this worked!