Closed-Reference clustered-table with all reference OTUs

Howdy! I’ve clustered some sequences from a study (not mine) to the GreenGenes 99% OTU database using cluster-features-closed-reference. However, the resulting clustered table only shows the frequency of GG OTUs that have been matched to the study sequences. Is there a way whilst clustering to generate a table that outputs rows for all ~200,000 GG 99% OTUs, even if not all OTUs are represented in the study sequences? My goal is to cluster sequences from other studies to the same GG database and then stitch the resulting tables together, so having consistency by representing all OTUs in each table would be ideal.

If you’re closed reference clustering OTU’s take their name from the database so you should be able to merge them together later.


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