Hi,
I have created an OTU table (ASV) using DADA2 script.
When I analyzed the different OTUs according to their sequences, I have noticed that some of them are resembled to each other (according to their sequences) in more than 97% and even more than 99% identity by using blast.
My question is why?
I went to get an OTU table which every OTU (ASV) is a cluster of 97% (identity of sequences).
I looked at the script again and I didn't see any parameter which allows to set the identity level in each OTU.
Am I missing something here?
p.s
When I used the assign taxonomy script afterward, I worked with the 97% db.
Tx a lot,
Nir
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Hello Nir,
Thank you for posting on the forums.
Yes!
OTUs and ASVs are different, and it sounds like you were expecting OTUs, and were surprised to get ASVs.
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis | The ISME Journal 
DADA2 makes ASVs, which can be different by only a single base pair! Your feature table contains ASVs, which is why some of them are very similar.
Let me know if that helps answer your question!
Colin
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Hi! If even after @colinbrislawn clarification you still want to work with OTUs instead of ASVs, you can cluster them at 97% of identity Clustering sequences into OTUs using q2-vsearch — QIIME 2 2019.10.0 documentation.
But ASVs are allowing to perform your analysis with higher resolution, IMHO.
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Hi Colin,
Thanks for your answer, I will read the reference to better understand this process.
Nir
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Hi,
I prefer to stay with ASV, as some of my analyses are related to species and strain levels.
I didn't realize that different clusters (ASV) could be similar to each other by even a single bp.
Thanks again,
Nir
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