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?