Hello sir

I have done open reference clustering (99% identity) for my sample. After taxonomic assignment, I got that taxonomy file and respective feature_biom_table (–o-clustered-table). In biom table 18336 otu id was there, whereas the taxonomy feature id was 39258. That 18336 otu id was present randomly among that 39258 id.
or_table.from_biom (12).txt (4.2 MB) or_taxonomy.tsv (4.9 MB)

Should I exclude the remaining the 20,922 feature id which has no corresponding otu id ?

Hi @Asha1,
It sounds like you are probably comparing the wrong files, i.e., the taxonomy corresponds to a different feature table. Make sure that you are assigning taxonomy to the clustered sequences if you want to compare those to the clustered table. I suspect you are comparing a clustered feature table vs. the taxonomy of unclustered sequences.

You could check the provenance of the QIIME 2 artifacts to make sure that you are comparing the correct files.

Good luck!