I have been happily converting biom -> tsv -> biom files using the tip from http://biom-format.org/documentation/biom_conversion.html#round-tripping-between-biom-and-tsv , 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: https://groups.google.com/forum/#!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.