Hi,
I am a little confused with ASV and OTU. After DADA2 we have a feature table (ASV) right? When i do the diversity analys the output is OTUs. They were convert into OTUs or it is more correct to say ASV insted of OTUs?
Thank you
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Hi @annsantos,
I think you’re talking about in q2-diversity when you calculate “observed OTUs”?
In that case, the Observed OTUs metric is just the number of observed features. If, instead of an ASV table, you passed in a gene table, the feature count would probably still be described as “observed OTUs”. Not because that’s what’s actually there, but because the metric is somewhat agnostic to what your features are representing.
So, if you’ve run DADA2 and passed in your DADA2 feature table, then what q2-diversity calls “observed OTUs” is really “observed ASVs”.
Best,
Justine
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Yes i am talking when I calculate qiime diversity. So, although the output of qiime diversity name be otus, they are in fact features?
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Yes! For alpha diversity, observed_otus == # of features
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when we do taxonomy assignment with greengenes database 13_8, then it is OTUs or still ASV?
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Still ASVs. The database will often use OTUs to define the names and groups, but that doesn’t change your data at all, you still have a mapping of ASV (feature) -> taxon. Please note, “feature” is the generic term for ASV, OTU, metabolite, MAG, etc.
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I get this confusion because of this: [Greengenes 13_8 99% OTUs], saying OTUs
Yep - this is what I was mentioning above:
These databases are often clustered into OTUs (for the example you listed above, 99% identity clustering). Again, this doesn't change your data. You still have ASVs, not matter what you label them taxonomically with.
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