Export to "classic" biom

(Natalie Gonzalez) #1


I was hoping someone here might be able to help me. I’m new to qiime2 so I’ll try to be as clear as I possibly can be with my limited knowledge of qiime2.
I’m running into an issue creating a classic OTU table. I’ve processed my sequencing data in qiime2 using the Moving pictures tutorial. I would like to create a classic OTU table so that I could import it into FUNGuild.

I went ahead and attempted to follow this tutorial.
I changed the headers of the taxonomy.tsv as instructed, and then I copied this file along with my exported feature-table.biom into a new folder. I then used the tutorial to run the following from within that folder

biom add-metadata -i feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp biom-taxonomy.tsv --sc-separated taxonomy

however when I exported the table-with-taxonomy.biom using:

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

the resulting tsv file looked exactly like my original feature table. Qiime2 didn’t give me any error messages so I’m not sure why this didn’t work. I’d appreciate any help figuring this out, and if it’s at all useful information I’m using qiime2-2018.8

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