Everything seems ok and I didn't run through any errors, but when I open my feature-table-withtaxon.tsv everything is messed up. I'll attach the files here so you can have a look what I'm talking about.
The command @thermokarst ran was meant to produce a .biom file not a .tsv file. I suspect you followed all the steps correctly, but gave your output file, feature-table-withtaxon.tsv, the wrong file extension. It should be a valid .biom file, but when viewed as a .tsv it looks corrupted and broken because .biom is a binary file format. Please change the extension on the file from .tsv to .biom and let us know if it works in your analyses.
thank you so much for the answer. That was indeed the problem, right in front of my eyes ARRGH!
It worked and I got a feature table with taxonomy.
The thing is that when I try to convert the table with taxonomy to .tsv, the tsv format stays exactly like it was before assigning taxonomy. I still get feature ID instead of taxonomy. I’ll have a look on some other posts, but if you have any ideas please share
It’s worth noting that when I give the command: biom head -i feature-table-withtaxon.biom, I get feature ID also, and not the taxonomy. So the problem is not on the conversion, but somewhere in assigning taxonomy?
I notice your feature table is also a .tsv, did you use this .tsv in the command you ran when attempting to create your annotated feature table? If so, please try again using the original feature-table.biom file.
Note that this time changing the file extension on that file from .tsv to .biom will almost certainly not work as feature-table.tsv is an actual .tsv, and you will need the original feature-table.biom you created before transforming it into a .tsv.
No, after your first reply I used the feature-table.biom to create my feature-table-withtaxon.biom following the steps provided by @thermokarst. But when I run biom head -i feature-table-withtaxon.biom I still get a table with Feature ID, and not taxonomy.
