Question: Can I use representative sequences from 16s RNA-Seq data to test if two samples have the same (or partially the same) bio-diversity?
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gravatar for tianlongapp
3.7 years ago by
tianlongapp10
United States
tianlongapp10 wrote:

Hi,

I'm new to 16s RNA-Seq analysis, and I have a question after using QIIME here.

For example, I have 2 samples from leaves with treatment of rain water collected at different time. QIIME results have shown that these 2 samples have similar bio-diversity of one bacteria family. Taxonomy assignments are done by clustering representative sequences with OTUs hence a threshold of distance allowing differences exists, in this case, is it reasonable for me to compare (BLASTN) the representative sequences of the 2 samples to see if they have the same (100% identity) representative sequences so that I can conclude that, say, Bacteria A from sample 1 is the same with Bacteria A from sample 2.

Thanks for responding. I would appreciate any answer or reference.

Edit #2:

Let me try to clarify my question a little more:

I want to see if one the microbiome community member of my 2 samples share the same origin (treated by different rain water). So I extracted the representative sequences clustered to the OTU of that bacteria species, and want to perform pairwise BLASTN to check the similarity of them. But I'm not sure if it makes sense.

qiime rna-seq microbiome • 1.4k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by tianlongapp10

Not sure exactly what you're asking, but qiime have their own very active forum which I'd check out as the developers are very reliable on answering queries: https://groups.google.com/forum/#!forum/qiime-forum

ADD REPLYlink written 3.7 years ago by Daniel3.7k

Thanks, but this is not very much related with QIIME itself I think, only representative sequences generated by it though. I will try it over there anyway.

ADD REPLYlink written 3.7 years ago by tianlongapp10

Let me try to clarify my question a little more:

I want to see if one the microbiome community member of my 2 samples share the same origin (treated by different rain water). So I extracted the representative sequences clustered to the OTU of that bacteria species, and want to perform pairwise BLASTN to check the similarity of them. But I'm not sure if it makes sense.

ADD REPLYlink written 3.7 years ago by tianlongapp10
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