Taxonomic assignment for 28S sequences

[avtober (Anya)]

Hi, I am looking into how to do a taxonomic assignment on my 28S data. It is hard to find any information on this as most people use 16S or 18S. I thought I could try qiime feature-classifier classify-consensus-blast and use the pre formatted silva database in the resources but it looks like that is only for 16S and 18S. How would I make a database for 28S. Is Silva the best database to use for 28S or would blast be better? I am also not sure whether it would be better to use sklearn and train classifier in this case.
Any thoughts on this would be greatly appreciated.

Thanks
Anya

[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

[avtober (Anya)]

Hi @SoilRotifer thank you for pointing out those threads, I will have a read.

Best
Anya