I am running v 1.39.5
Using Silva full 132 for alignment
silva 132 and pds16 for taxonomy, cutoff 70
I used vsearch for clustering (yea I know)
I have a mock community containing Salmonella
When I use classify.seqs, I see Salmonella sequences being classified.
When I use classify.otu, I do not see them anymore!
It was working fine before. Changes made: use to use Silva v128.pcr for alignment, classification cutoff of 80, Silva v128 for taxonomy (had a hard time finding Salmonella) and PDS 16 (was finding Salmonella with ease).
Could it be a cluster problem? (My bet is on this, but weird since I never had this problem)
Or should I lower once more the cutoff for classification to 60?
Or anything else?