Hello again (apologies for so many posts lately),
To analyze18S v9 sequences, I have made a few substitutions for reference sets. For instance, I am using silva.nr_v132 instead of silva.seed
I also used trainsets16_022106.pds instead of trainset16_022016.rdp side question, why switch from silva to rdp at this point in the analysis?)
After running ‘classify.otu’, however, almost all levels of the taxa have shown up as ‘Eukaryota_Unclassified’. Could this be due to the reference datasets I have used not containing enough 18s sequences?