Hi, can I prepare a taxonomy reference without Chloroplast, Mitochondria, unknown, Archaea, Eukaryota for classify.seqs. Then, any reads from them will be classified as ‘unknown’ and can be removed later. I guess this may save some CPU time which can be significant given large data volume.
Thanks a lot.
For Chloroplast, Mitochondria, Archaea and Eukaryota it would be as simple as passing remove.lineage() over your taxonomy database. You can’t get rid of ‘unknown’, because that’s mothurs keyword for sequences that can’t classify to anything in the database.
That said, I’m not sure this will work the way you’re expecting - if you remove Chloroplast from the database you’ll still have the Cyanobacteria that these nest under and might just find that sequences that would have become Cyanobacteria;Chloroplast become Cyanobacteria;unclassified and don’t get filtered out.