Identifying bacterial taxa (16S) that correlate with eukaryotic taxa (18S)

[Nicholas_Bokulich]

Hi @rachaellappan,
I would recommend checking out q2-SCNIC or another tool (like spieceasi, not yet implemented in QIIME 2) for doing correlation/network analysis. These are designed for this type of comparison, relieving some of your concerns about data dredging and the appropriateness of the tests you use.

Since you are specifically interested in Blastocystis, you could also make a PCoA biplot as described here:

How to use pcoa-biplot

Hi @suzukik! Great question, there’s a few steps to this: Use qiime feature-table relative-frequency to generate the table for pcoa-biplot. You need this to be based on the rarefied table you are using for your beta and pcoa steps. You can use provenance to prove that you’re using the same rarefied table in both relative-frequency and pcoa Run pcoa-biplot with that table and an existing PCoAResults (generated by your previous pcoa). Use qiime emperor biplot with --m-feat…

But SCNIC or speaceasi would allow you to identify more connections between the 16S and 18S data.

Good luck!