Question: Can I convert a species to otu?
gravatar for jeremy.cox.2
20 months ago by
United States
jeremy.cox.290 wrote:

In one hand, I have OTU data from 16S, which can be graphed in a cladogram-like format. (My colleague generates this.)

On the other hand, I have species counts, which can be graphed as a cladogram.

I want to do a fair side-by-side comparison.

I am pretty sure we can't convert OTU to species or genera with 100% certainty.

However, it seems if OTU are predefined, then there should be a mapping somewhere of species to OTU. Is this possible? How would I do it?

taxonomy 16s otu • 429 views
ADD COMMENTlink modified 11 months ago by lakhujanivijay4.4k • written 20 months ago by jeremy.cox.290
gravatar for lakhujanivijay
11 months ago by
lakhujanivijay4.4k wrote:

Technically , taxonomies could be assigned by comparing 16S data ( I.e. OTU in your case ) to publicly available databases like green genes or SILVA. However, with a small stretch of gene like 16s, it will be unfair to declare taxonomies up to species level. The reason for that is, there are many organisms which do share high degree of similarity for this gene , but taxonomically they are very much different at species level. There are also cases where 16s regions are quite different but the spices or genus is same. Hence, a classification upto family level is acceptable , and further assignment down the taxonomic domains is a matter of careful consideration, analysis of other marker genes and wet lab validations. By the way, OTU itself is a highly mis understood term, with vague and often mis used meanings.

ADD COMMENTlink modified 11 months ago • written 11 months ago by lakhujanivijay4.4k
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