Converted biom table does not contain taxonomy

[Pablo_V]

Hi,

I am trying to obtain a classic OTU table with taxonomy using the biom functions from qiime2. I have followed the post by @thermokarst (Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)) and when I obtain the biom table with taxonomy, I try to convert that biom table to tsv format and the taxonomy annotations are not added!

I have checked other posts with similar problems:

• Basic questions regarding classic OTU table in QIIME2 --> Here the error was not adding “#OTUID taxonomy confidence” to the taxonomy.tsv file. However, I have changed the headers accordingly.
• Exporting feature table and adding taxonomy and converting to tsv --> Here the error was not adding “–header-key taxonomy” when converting the biom table into txt format. However, I have added “–header-key taxonomy” when converting the biom table with taxonomy into txt format and I get the following error:
  …
  ‘sc_separated’: lambda x: '; '.join(x),

TypeError: can only join an iterable

So, could anybody tell me how to fix this issue?

Cheers,
Pablo

[Mehrbod_Estaki]

Hi @Pablo_V,
I haven’t actually looked into your specific error/case here but a while back I did write a mini-tutorial on how to go from a qiime2 feature-table to a BugBase compatible OTU table and the first portion of it I think does what you want to do. Do you want to try that and if that doesn’t work for you then we’ll come back to troubleshoot this properly.

[Pablo_V]

Hi, @Mehrbod_Estaki,

I have followed the indications from the link you suggested and now it works perfectly! Thanks a lot.