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Filtering FASTQ Files
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.
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GenoMax
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cbrown58 •
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1 answer
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.
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