I am trying to use a biom table that was built using Qiime 1 in order to generate alpha and beta diversity plots on Qiime 2.
The issue is that I do not have the sequence files or the phylogenetic tree (although the biom table was built using closed OTU picking with green genes database). Is there a way for me to work around this and still use QIIME 2 to generate alpha/beta diversity?
We should get you playing around in qiime2 no problem.
I will first say though if you do happen to have the raw reads from this project, I would certainly recommended starting right from those in qiime2. But assuming that is not an option let’s see how we can get you sorted.
First you’ll need to import your .biom file into qiime2 using the options listed here. Next we’ll need to build a tree in order to perform phylogenetic-based actions. Usually this is done using the representative-sequences you would get after OTU picking or denoising in qiime2, since I assume you don’t have this let’s bring in the next best thing.
Luckily, the fact that your .biom table was made using closed-reference OTU picking from GG should make things easy for you! Download the greengenes files from here then you can either import the actual premade tree from Greengenes that matches your OTU picking % identity, or import the Greengenes rep-seqs that matches the percent % used in your OTU picking and create a tree based on those in qiime2. Either one would work. In all cases, see the importing tutorial link from above how to import these files.
At the end of this you should have a feature-table, representative sequences, and a tree that you can use for all your alpha and beta diversity analyses in qiime2.
Hope that helps.
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