Results consensus when analyzing many V regions

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#1

Hello all!
How are you? Happy new year!! :partying_face:

I am analyzing my samples with Ion Torrent sequencer and have the following question. The thing is that the kit sequences 7 hypervariable regions and I want to compare the results I get in Qiime2 (about those 7 regions) with the ones obtained using the Ion Reporter software.

This Ion Reporter software gives the taxonomic results by regions or using a consensus of all the regions, where the results of each regions are added up. My questions is if the command classify-consensus-vsearch does a similar consensus or not, as I am analyzing 7 regions instead of one.

Thank you so much in advanced :smiley:

#2

Happy new year to you as well @MiriamGorostidi!

The “consensus” in this method stands for something else: it means that the taxonomic ID (of each individual read) is assigned based on the consensus taxonomy of the top hits, not a consensus of the separate regions (which sounds more like a sum of the results from each read, rather than a consensus per se based on your description).

But the equivalent could be accomplished, by using the full-length 16S rRNA gene sequences as a reference and analyzing all the data together.

This and other related topics are discussed in this long but informative topic:

Good luck!

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#3

Thank you Nicholas!

Yes, I had seen this topic and I have already run those steps with my data. I only needed to know what that “consensus” stood for.

Thank you so much! :slight_smile:

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