While I normally use ASVs from Deblur, I would like to have a look at OTUs clustered at 98 and 95% similarity. Following tutorials, I’ve put together some scripts, but I need some help to fix them. I am not sure right now how to link the clustering step to the GreenGenes database that I am using. Here is an example:
qiime vsearch cluster-features-open-reference
My issue is that the GreenGenes database only has otus clustered at 94, 97 and 99. I was wondering how proper it would be to associate --p-perc-identity 0.95 with the closest reference OTUs (e.g. --i-reference-sequences path2files/ref.otus.94.qza), or should I rather go down the de novo clustering route. I would then still assign taxonomies using the most similar reference dataset (i.e. reference 97% OTUs for 98% clustering, and 94% OTUs for 95% clustering).
Thank you for your kind attention, and I look forward to your feedback,