Taxa names (each letter) are separated by semicolons after merging feature-table and taxonomy

Good day!

It is my first time to use QIIME2. As I create OTU table with the taxonomy metadata and feature counts of my samples in QIIME1, the taxon names (each letter) became separated by semicolons (please see attached file) when I convert the biom file into tsv file.

JBfeature-table_withtaxonomy.tsv (2.3 MB)

I used this command:

biom add-metadata -i denoisetable/feature-table.biom -o feature-table_with taxonomy.biom --observation-metadata-fp taxonomy97/taxonomy.tsv --sc-separated taxonomy --float-fields Confidence

At first, I thought it was because of --sc-separated, but I also tried not to include --sc-separated but the result is the same.

What should I do to fix this thing? Thank you very much in advance.

Hi @jakebaquiran! Take a look at this forum post, where I show how to export a feature table and taxonomy data from QIIME 2 and import that data into a .biom file (e.g. for use with QIIME 1 or another tool).

We don’t support the biom or QIIME 1 tools on this forum, so we’ll be limited in our ability to help you past exporting your data from QIIME 2. If you have further questions about those tools, you should post to either the QIIME 1 Forum or the biom-format issue tracker. Thanks!

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Thank you very much @jairideout for your help.


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