Taxonomic assignment for 28S sequences

[SoilRotifer (Mike Robeson)]

Hi @avtober,

If you search the forum you'll find several threads on obtaining and formatting SILVA LSU data for QIIME 2. Here is one of the more recent threads:

Weird Taxonomic classification 28S rRNA

I can’t really say, it is largely dependent on the sequence lengths present within the SILVA database. You can also simply filter everything to the same length too via filter-seqs-length. Also, one option is to not filter based on length at all until after you’ve extracted your amplicon region first. That is, you may remove short “full-length” sequences which actually contain your complete amplicon region. We allude to this in the tutorial: As for your next question… The SILVA 138 LSU was n…

-Good Luck!
-Mike