We are getting ready to submit a paper for publication and the figures I have made include relative abundances of bacteria at the Genus level for each patient sample from the Mothur OTU output. There has been some heated debate about the unclassifed reads. Most samples have about 2-4% of reads that can’t be classifed at the Genus level but there are about 3 samples that have about 50% of their reads unclassified. Some people in my group want to remove all of the unclassifed reads. Does anyone know how to approach these unclassifed reads or have an opinion? The concern is that when I make a dendrogram the unclassifed reads obviously affect the clustering of the samples.