How to include confidence in taxonomy-annotated BIOM file?

(Natalie Gonzalez) #1

Hi all,

So I’ve followed the example listed above and the new .biom file that I export is great, but the confidence isn’t in my exported file. I have column 1 containing my #OTUID, the next columns containing my samples and reads, and the last column contains the taxonomy but no confidence values. I’m clearly missing something.

This is what I’m running if anyone is able to help:

biom add-metadata -i feature-table.biom -o table-with-taxonomy3.biom --observation-metadata-fp taxonomy_reformatted.txt --sc-separated taxonomy

biom convert --input-fp table-with-taxonomy3.biom --output-fp table-with-taxonomy3.tsv --to-tsv --header-key taxonomy

Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)
(Matthew Ryan Dillon) assigned thermokarst #2
(Matthew Ryan Dillon) #3

I am not a biom developer, but, I found this little nugget, w.r.t TSV-style BIOM files:

the classic format can support only a single observation metadata entry

As I understand it, you can have the taxonomy annotation, or the confidence value, but not both. A workaround might be to collapse your FeatureTable[Frequency] in QIIME 2 with your taxonomy (check this example, at the very end of the ANCOM section), before exporting to biom.

You could just metadata tabulate your table and taxonomy and grab the TSV out of there (thanks for pointing out the error of my ways, @Nicholas_Bokulich)

(Matthew Ryan Dillon) unassigned thermokarst #4