Comparison of Similarity Between Two Different Datasets


I have been able to follow the “Moving Pictures” tutorial (which is a phenomenal resource!) to perform some really interesting data analysis so far, but I want to see if I can make any additional useful comparisons. Since I’m working with the microbiome of salamanders, I want to compare my data to cutaneous bacteria of amphibians which comes in the form of a .fna file from the following link:

Ecological Archiles E096-059-D1

I have performed everything in the “Moving Pictures” tutorial on my personal data, so I have a ton of different file types to work with (e.g. rep-seqs, de novo clustered rep-seqs, tables, filtered-tables, and more). I was wondering if there was a way with qiime2 to look at the similarity between the two sets of data. So far, I’ve only imported the .fna of the common amphibian cutaneous bacteria as a FeatureData[Sequence] artifact and a FeatureTable[Frequency] artifact but have not done many different transformations to it (because I don’t know if there’s a way for me to compare them yet).

My question lies in if there is an existing way to directly take two different sets and compare, or if there’s a way to integrate them into one mega dataset and then run internal analyses based on metadata columns. In the event there’s not a way to do so in qiime2, could anyone point me somewhere where I’d be able to do such analysis?

Thanks so much, and have a wonderful day!

Use qiime feature-table merge to merge the two feature tables, then analyze (as shown in the tutorials) using metadata columns that differentiate these datasets. Check out the FMT tutorial for an example of merging tables and sequences from two different runs.

Good luck!