QIIME2 to PICRUSt

[ellen]

Hello, I am working on using PICRUSt after QIIME2 analyses. I am having some trouble though. I have been trying to use the exported feature table for my analyses (a .biom file). But that does not contain taxonomic data. I have been trying to add that data by exporting the taxonomy.qza file then using the biom add-metadata command. This has not been working though. The command runs but the taxonomic data is not added to the .biom file. Does anybody have any insight?

[Nicholas_Bokulich]

Hi @ellen,
Have you seen this tutorial?

Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)

Creating a TSV BIOM table The following is based on a post by @gregcaporaso. $ qiime tools export table.qza --output-dir ./ $ biom convert -i feature-table.biom -o feature-table.tsv --to-tsv $ biom head -i feature-table.tsv # Constructed from biom file #OTU ID L1S105 L1S140 L1S208 L1S257 L1S281 4b5eeb300368260019c1fbc7a3c718fc 2222.0 0.0 0.0 0.0 0.0 fe30ff0f71a38a39cf1717ec2be3a2fc 5.0 0.0 0.0 0.0 0.0 d29fe3c70564fc0f69f2c03e0d1e5561 0.0 0.0 0.0 0.0 0.0 868528ca947bc57b69ffdf83e6b73bae 0.0 227…

That would be the best guide to follow from QIIME 2 to picrust.

The issue you are having is with biom-format, not QIIME 2, though, so we may have limited capacity to help debug if that tutorial doesn't lead you down the right path.

Let us know if that works, and if not please post the full commands and we might be able to help!