frequencies of feature per sample

[chiara (Chiara Conte)]

Dear All,
I recently move from qiime1 to qiime2 and I find qiime2 much better and cool. However, I have some doubts regarding the output I can get.
I used to work with the OTU table in the downstream analyses within and out of qiime1.
It is not clear to me how I can obtain the corresponding OTU table in qiime2, whereas a table where I can see the frequency of each feature in every sample. So far, I have obtained just the overall frequency of the features.

I apologize whether I am missing some steps.
Thanks in advance!

Best

[jwdebelius (Justine Debelius)]

Hi @chiara,

The artifact you're looking for is the feature table. (Sometimes called an ASV or OTU table). It has a semantic type FeatureTable[Frequency].

If you want to move directly to R, I recommend qiime2R. The python API is great if you're a python person. There's also a tutorial for converting to text.

Best,
Justine