Hello there,
My Fungal sequences (ITS) were assigned to taxa using the naive Bayesian classifier against the UNITE-curated International Nucleotide Sequence Database reference database, and the output obtained revealed 80% of the OTUs assigned to unclassified fungi. My samples are from mosquitoes, I really need help on how to assign the remaining 80% assigned as unclassified.
Hi akuaFO,
Based on my experience, using ITSxpress to extract only fungal sequences could be a good solution for your issue. It helps refine the data and may improve the taxonomic classification by focusing on the ITS regions specific to fungi.
Best regards,
Soyeon Kim.
Hi @akuaFO @soyeon_kim and welcome to the 
Forum!
I definitely agree with that! ITSxpress removes conserved regions that do not help when we assign taxonomy. However, 80% of unclassified sequences seems like a lot for me! IMO, something else is happening here.
@akuaFO , would you mind sharing with us the UNITE version you used? I suspect those results come from a taxonomic classification using the only fungi UNITE version instead of the all eukaryotes. What do you mean exactly when you say your samples are from mosquitoes? What organisms do you expect your ITS sequences to be from?
Best,
Sergio