QIIME2 ASV Table for PICRUSt (Galaxy)

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To Whom It May Concern,

Attached in this email, is an ASV table (with taxonomy information) that I am trying to run through PICRUSt (on galaxy, https://huttenhower.sph.harvard.edu/galaxy/). However, I am getting an error, that I assume has to do with the Greengenes database that was used to generate my file. The error is below:
PICRUSt requires an OTU table reference/closed picked against GreenGenes.
Example of the first 5 OTU ids from your table: 8ef7209537fc461aceaba8148eadb2bf, 6ed0b06fef96382a9fc1b8220f18acf0, d99d7fc3d64d5b33656bcf5f793152dd, 80061880f0b4ff3e3c63ed98f8d69541, 9afd7bbb556474ce3f86e2f7befa1f81

Is there a strategy for solving this error?

picrust.txt (457.2 KB)

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Yes, you need to run PICRUSt against Greengenes. It should go through closed picking via vsearch rather than you DADA2 file.

This is the same error when you run it using open or de novo picking in QIIME1. I would recommend you do a greengenes run with your file.

Ben

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Thanks Ben for the suggestion. I also came across this informative [Picrust support?](http://PICRUSt support advice).

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Hi @DoHarris,
I wrote a mini-tutorial here on how to get your data ready from ASVs format to BugBase compatible. Since BugBase runs PICRUSt in the background I imagine this would should work in your case too. Would love to know if this works for PICRUSt1 too.
That being said, have you considered using the new updated PICRUSt2 instead which works with ASVs and isn't reliant on the greengenes database. Conveniently, it has a q2 plugin as well.

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Hi @Mehrbod_Estaki,

I have never used PICRUSt2 or BugBase. I have skimmed through the BugBase pre-print and I am pleased to say that I'd love to use the software. In case I have additional questions, I will get back to you. Many thanks.

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