Finding common species between two studies


I have 2 studies (each with paired-end demultiplexed fastq files). I analysed each of them separately and I have the finished the taxonomic classification step for both the studies. I am interested in finding species that are common to both the studies (the names and count if possible). Can I do so in QIIME2? If No, can it be done through R programming? How?

Any suggestion is appreciated!

Hi @SAHIL_JAIN_16110144,

The answer depends on whether or not they are from a similar hypervariable region. If they are, I would trim so they start at the same basepair and are the same sequence length, and then you can just merge the table and rep set. You will, I think, need to rebuild your tree because although it should be stable, you might see some shifts. Im not sure if the taxonomy can be concatenated, hopefully someone with more experience there can comment.

If the studies were sequenced using different hypervariable regions, you will need to pick both closed reference against the same database.


The studies are from different hypervariable regions. I did de novo clustering of each of the studies and then compared them with the same database (final output after this step: taxonomy.qza file for each study). I am interested in finding the shared OTUs between these two studies.
Does this make my question more clear?

Yes, that makes it clearer!

Unfortunately, best practices now say that you need to pick closed reference against the same database if you want to make a comparison of different hypervariable regions. So, that would be my recommendation.

I’ll also mention that hypervariable region has a massive effect on the data, and you’ll likely see an impact there, so I’d think about maybe phylogenetic or aggregated-based comparison rather than OTU to OTU.


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