Extract fasta sequnces not matching a list
Hey guys,
I know it's possible to use seqtk subseq to extract fasta files matching a list. Now, is there a way to extract those fasta files that don't match the exact fasta headers on the list? Thanks!
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GenoMax
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genomes_and_MGEs •
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genomes_and_MGEs •
1 answer
You can use faSomeRecords from Jim Kent's utils for that.
faSomeRecords - Extract multiple fa records
usage:
faSomeRecords in.fa listFile out.fa
options:
-exclude - output sequences not in the list file.
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Looks like you already have a solution. In general, this boils down to list manipulation. If you have a list of all sequences and a list of those that you don't want (those to exclude), grepping the two files using a
-voption will give you their difference that can be used in normal fashion.