Can I combine fungal ITS and bacterial V4 microbiome analyses?

[colinbrislawn (Colin J Brislawn)]

Hello Anka!

Welcome to the forums.

@anka

Is there any way to complete this in QIIME2 or in R?

Yes, you can merge features tables in both Qiime2 and Phyloseq. However, combining data from different regions is hard. That thread is about different regions of the 16S gene, and the problems are the same for your 16S V4 and ITS reads.