Converting and exporting (.tsv to.biom)

[conhow (Connor Howard)]

Hi there,
I am very new to Qiime 2. I am wanting to convert a .tsv file I have containing an OTU table that was filtered to contain only reference OTUs only, to a .biom file. Then I would like to export that .biom from Qiime 2 and use it with Picrust. I cannot seem to get biom convert to work and I am unsure of how to export the .biom file if I were able to convert it.
Thanks

[thermokarst]

Hi @conhow!

@conhow

I am very new to Qiime 2.

Welcome!

@conhow

I am wanting to convert a .tsv file

We have an open issue to support directly importing this kind of BIOM table, but for now, your workflow makes sense.

@conhow

I cannot seem to get biom convert to work and I am unsure of how to export the .biom file if I were able to convert it.

Did you take a look at the BIOM docs? It looks like you should be able to run something like the following to convert your TSV BIOM file to an HDF5 BIOM file:

biom convert -i table.tsv -o converted_table.biom --to-hdf5

Then, you can check out the QIIME 2 Importing tutorial for information on how to import this file!

Let us know how that goes for you, and if you get stuck, you know where to find us!