classify.otu: differences between threshold and cutoff


I am trying to understand the differences between threshold and cutoff …(sorry I am having trouble understanding the definitions on the website…)

For example in my last.0.03.cons.taxonomy I have:

Otu00004 84236 Bacteria(100);Bacteroidetes(100);Flavobacteriia(100);Flavobacteriales(100);Flavobacteriaceae(100);Polaribacter_4(52);

So my understanding is that the confidence interval of this Otu to belong to Polaribacter is only of 52% ?

So if I wanted to remove such a low confidence interval I should use cutoff=80?

I added this on the code and it did not change anything …i tried threshold =80 and no difference either…

I would like in this instance not to get Polaribacter since a 52% confidence interval is low (?)



When you run classify.seqs the numbers in parentheses are the confidence scores from the classification algorithm. WHen you run classify.otu (what you have here) the numbers in parentheses represent the percentage of sequences in the OTU that have that classification. If you want to set a threshold (and you should), that should be in the classify.seqs step.