I'm a new user to Qiime2 tools, and I'm currently trying to extract the taxonomy file from a biom table. I have found tutorials that go the other way, i.e. exporting taxonomy files and add them into a biom file. But I have a biom file right now and would like to get the taxonomy information as a tsv or tab-separated txt. How can I do that?
Thanks for any help!
Hello and welcome to the forum!
I am a liitle bit confused - what is an origin of your biom file? Did you create it in Qiime2 workflow? If yes, then your taxonomy information should be in the taxonomy.qza file (if you already performed taxonomy classification step in qiime2), not in the biom. You can use export command from Qiime2 to export taxonomy.qza file as a .tsv table.
If you you have a biom file, created outside of the qiime2 and which includes taxonomy information, then use the commands from the tutorial you already found to convert this biom file into .tsv and separate count table and taxonomy into 2 different tables if needed.
Thanks for the reply! I obtained the biom file from Qiita database which I believe uses Qiime2 pipeline for processing as well? But I'm just getting the biom table off of Qiita and wondering if I can extract the taxonomy file from that. I haven't been able to find the biom commands to do so.
You can convert biom file to tsv:
biom convert -i table.biom -o table.tsv --to-tsv
Then you can check if this tsv file includes taxonomy annotations by opening it in Excel or Calc.
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