I have a question regarding my beta diversity (Bray-Curtis) where my four controls cluster close together, yet looking at the taxonomy bar plot they show abundance of different species. I am most likely missing something in my analysis.
Method to get to the results was:
Quality and primer trimming with cutadapt
DADA2 denoising
de novo clustering with VSEARCH at 97%
phylogenetic diverisity
Taxonomy classification was done by training Greengenes classidier.
Hi @Bojarski,
Sometimes the world works in myserious ways. My reading of this is that even though you see different species in the control samples, they are still much less dissimilar to each other than they are to the other samples. In other words, your control samples are clustering together because they still bear more resemblence to each other than they do to the other samples.
