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primordialsoup77 12-03-2013 06:31 PM

Appropriate to assign taxonomy to OTUs?
This may reflect my misunderstanding of taxonomy-dependent and independent methods more than anything, but here is a question I have. If I have sequencing data from an environment that is well-characterized (i.e. well-represented in databases like RDP, Greengenes, SILVA, etc.) then TD classification methods are appropriate, correct? However, if the sequences are not well-represented, then some or all of the data would be analyzed using TI methods. So why is it appropriate (or inappropriate) to then turn around and assign taxonomic labels to OTUs, even if based on a "representative sequence"?

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