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jtpoirier / proteomegenerator

Proteome Generator
MIT License
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Check that use of BLAST's `-max_target_seqs` is intentional #6

Open acesnik opened 5 years ago

acesnik commented 5 years ago

It looks like this confusing parameter is often misused. See https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166

jtpoirier commented 5 years ago

Thanks, I was not aware that this parameter behaved this way. You may also want to raise this issue w/ Brian Haas, the TransDecoder author. In the current application, the point is not necessarily to get the "best" hit, but to rescue ORFs that have any uniprot hits below a given expect value so that they aren't discarded.

acesnik commented 5 years ago

Looks like it's already an open issue https://github.com/TransDecoder/TransDecoder/issues/74