Convert tsv to biom on collapsed taxa table


I have been happily converting biom -> tsv -> biom files using the tip from , but I found this only works for feature tables that were not taxa collapsed (i.e. in their original OTU IDs). I’d like to do the same thing for feature tables that were collapsed using qiime taxa collapse, but I got an error during biom convert saying “Duplicate observation IDs”. Someone has the same problem as me:!topic/qiime-forum/DmQ9s6Bptsk (his .tsv file is taxa collapsed). My goal is to convert back to biom and then re-import as a collapsed taxa table. Is there a convenient tsv -> biom conversion for this? Thank you.

Hi @jjmmii,
Sounds like this error is occurring with BIOM, rather than QIIME2, so support for BIOM should still be posted to the QIIME1 forum (where you found the related forum post).

However, maybe we can help you find a way to avoid exporting your feature tables and “round tripping” (i.e., do it all in QIIME2). The process you describe will cause your artifact to lose all provenance, which can be inconvenient if at a later date you are trying to trace your steps and figure out what you did with that file!

So that leads me to ask — what are you trying to accomplish?

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