mothur

OTU and ASV in taxonomy file

Hello all.

I do not want to start any debate on OTU or ASV.

But I think it would be great to be able to have a taxonomy file that would look like: ASV; OTU; genus; and so on.

My problem is that I am kinda stuck sometimes to use ASV as some of my favorite bacteria (Salmonella for example) is getting clustered with another sequence and is thereafter disseapering since it is not the selected representative sequence. I saw this happens with my dear salmonella, so I think that some other bacteria get the same treatment.

So if I could have the taxonomy made from the ASV but still be able to use OTU, that would be awsome.

Thanks - I’ll add it to the list of future features. In the mean time, if you know R, you could likely do this with different joins on the sequence and its ASV/OTU/taxonomy assignments

Pat

ok, I will see how I can do that. I knw a bit R, enough to be functionnal but on the top of my mind I do not know exactly how to do this!

I will post here went I take the time to try to find it! hehehe.

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