Hello,
When I look at the Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.tax.summary file, I am a little confused about the classification of the OTUs. There are some OTUs that are classified as the same with a 100% confidence threshold. Eg:
OTU1: Otu00001 22860 Bacteria(100);“Bacteroidetes”(100);“Sphingobacteria”(100);“Sphingobacteriales”(100);Cytophagaceae(100);Microscilla(100);
OTU13: Bacteria(100);“Bacteroidetes”(100);“Sphingobacteria”(100);“Sphingobacteriales”(100);Cytophagaceae(100);Microscilla(100);
I am not sure how to interpret this, especially if I am interested in knowing the most abundant species in some of my samples. OTUs were constructed at 97% similarity. Therefore, shouldnt the two Microscilla be included under the same OTU?
Thanks