Exporting feature table and adding taxonomy and converting to tsv


(Burhan Shamurad) #1

Hi
Thanks for accepting me to qiime2forum.
i tried to add observation taxonomy metadata to the feature-table.biom , everything looking good but when i convert the biom file to tsv i cant see taxonomy added to the feature biom file…can you help please
i followed all the stages suggested by https://forum.qiime2.org/u/thermokarst


Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)
(Nicholas Bokulich) #2

Hi @burhan_shamurad,
Check out the biom-format conversion instructions. Make sure you use --header-key taxonomy (or whatever the taxonomy header key is labeled) when you convert to tsv.

This is an issue with biom-format, not with QIIME 2, so I am not too familiar with troubleshooting this if that does not work.

I hope that helps!


(Burhan Shamurad) #3

Thanks Nicholas…
yes i added --header-key taxonomy its worked now.

But some sometimes instead putting taxonomy on the last column it puts taxonomy under the first column and named #OTU ID instead of taxonomy…very strange to me …


(Nicholas Bokulich) #4

As far as I know, that should only happen if your feature table was “collapsed” (e.g., with qiime feature-table collapse) based on taxonomic classifications, and biom should not do that during metadata annotation or conversion.


(Burhan Shamurad) #5

Thank you so much…I followed your suggestions …now its working correctly.