I have bees trying the different methods to taxonomic classifiers in Qiime2. I have data from PGM Ion Torrent and I amplified a fragment of18S gene. I used all time Silva 128 database to compare my sequences.
My results with blast and usearch were fine, and the results with sklearn was not very good (maybe because I could not specify there that my sequences can be in plus or reverse direction form the PGM).
Then I tried open reference otu picking from Vsearch, and I got my feature table. Following the recommendations of other topic in this Qiime2 forum (closed now) I convert my feature table to biom and then to tsv, in order to check how is the table and how much similar is respect to the otu-table from QIIME1.
The feature table is exactly the same than in QIIME1, only change the name of he newreferences (now with a code). However, I do not have the taxonomy in my last column, after all columns of my samples, so I have the accession numbers that correspond with my sequences in Silva database but not the taxonomy (really the interesting part).
1- Could I use the comand biom-add metadata to add my taxonomy? in that case, what’s happen with the sequences called like “new sequences” (because is open-reference-analyses)?
Thank you very much for your help in advance!