Converting biom to classic format?

Question

Is it still possible to convert .biom tables from QIIME to QIIME’s "classic" OTU table format to use with Explicet? I've tried running the command from biom-format.org

biom convert -i table.biom -o table.from_biom_w_taxonomy.txt --to-tsv --header-key taxonomy

but gives back an error:

biom convert: error: no such option: --to-tsv

Any ideas?

Answer 1

I'm using QIIME too and went through the tutorial from Wernerlab. Here I've successfully converted a .biom table into a text file, also with the biom convert command. Maybe you can find clarification in the command line there:

biom convert -i otu_table.biom -o otu_table_tabseparated.txt -b --header-key="taxonomy" --output-metadata-id="Consensus Lineage"

Cheers, Dennis