I'm currently comparing taxonomy results for ITS1 sequences derived from sediment samples (amplified using ITS1F/ITS2), obtained using three different naive-bayes classifiers (trained in qiime2) using the following reference datasets:
- UNITE v 8.3 dynamic all eukaryotes (qiime release)
- UNITE v 8.3 dynamic fungi (qiime release)
- NCBI BioProj 177353 (Fungal ITS) trained using RESCRIPt
I've attached the resulting taxonomic comparison for your reference.
taxonomy-compare.txt (4.1 MB)
Although there is generally good consensus between these classifiers, one major difference I see is that the all eukaryote UNITE classifier returns "Unassigned" classifications (with various confidence values) for many of my features, while the fungus-specific UNITE and NCBI-ITS classifiers return "k_Fungi" (confidence value = 1) for almost all of the same features. Is the "k_Fungi" kingdom classification to be trusted or does the "1" confidence value here actually somehow indicate the opposite of 100% confidence - that these should be considered "unassigned" like the UNITE eukaryote classifier is saying?
I've scoured the forum, but was unable to find anyone with the same predicament. Before considering these features as poorly classified fungi, I want to make sure they're not actually erroneously classified coamplification of some kind. I appreciate your input regarding how I might best answer this question using QIIME2.