Differences in the depth of the taxonomic assignment

qiime2-r

#1

Hi there,

I am using the qiime2R package to import .qza files into R, follwing this tutorial and it works fine. I want to create a phyloseq object for further analysis.
However, I have differences in the depth of the taxonomic assignment in my taxonomy.qza file which makes it not possible to use the code of the tutorial to get a nice taxtable.
I tried to use the qiime taxa collapse command to collapse to an even taxonomic depth, but if use this comand the Feature.ID gets replaced with the taxonomy so I don’t know how to use this to create a phyloseq object.

Is there any solution that I can create a phyloseq object even if I have differences in the depth of the taxonomic assignment in my taxonomy.qza file?

Thanks in advance!

Samuel


(Nicholas Bokulich) #2

Hi @samu,
See this tutorial for exporting and annotating a biom table:


That should be importable as a phyloseq object.
Good luck!


#3

Dear @Nicholas_Bokulich,

This solution worked fine. Thank you for your prompt support. It’s greatly appreciated. :blush::tada:

Best,

Samuel