Phylotype approach

slaperriere · March 2, 2015, 4:11pm

Hi -

I am processing some MiSeq 2x150 runs of the V4 region. Due to the high error rate, I am taking the phylotype approach. When using the phylotype command, do sequences that don’t identify past a certain level get binned together? For example, my most abundant OTU is an unclassified bacteria. Are the the sequences in this group similar? Or do they bin together even if they are dissimilar because they don’t get identified past bacteria?

Thank you!
Sarah

pschloss · March 6, 2015, 4:31pm

If you have a bunch of sequences that classify as unclassified Enterobacteriaceae (or any other level) they will form a genus-level phylotype together.

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Phylotype approach

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