Importing ASVs to R (Phyloseq package)

[Mehrbod_Estaki]

Hi @OBrodnicke,
Welcome to the forum!
Check out this awesome tool for importing Qiime2 data into R and even directly to phyloseq.

@OBrodnicke

Is there a way to create a table that have the freequences of sequences anotated to the highest taxonomic level possible AND including what ASVs make up those assignment?

There isn't an option for this in Qiime2 though your taxonomy visualization can easily show which ASVs belong to which group; these don't have the frequencies though. You'd have to customize something in R to accomplish this since its a very specific request. From memory I don't think this exists in Phyloseq either but you might want to ask about that on their github page.

@OBrodnicke

Alternatively I could immagine a feature table only with ASVs (not taxonomically assigned) would be enough as imput for the Phyloseq package.

This is in fact the best way to do this in Phyloseq. You provide it with a feature table of ASVs and separately provide your taxonomies then use tax_glom to choose which taxonomic level to analyse your data at within each script.

If you do make a script or find an easy way to accomplish what you described feel free to share it here, would certainly be good to have around!