exported .biom format file qiime2

[Dani (Daniele)]

Hi All,
I hope you are well. I am using qiime2.2019.04 version.
I am trying to exported .biom format file to use in the Microbiomeanalyst, but unfortunately I did not find enough explanations in the Forum for me to succeed without asking about. Maybe can you help me?

The only information I found on the internet was as follows:
#first, export your data as a .biom
qiime tools export
feature-table.qza
–output-dir exported-feature-table

#then export taxonomy info
qiime tools export
taxonomy.qza
–output-dir exported-feature-table
#then combine the two using the biome package (dependence loaded as part of QIIME2 install)

Any ideas on how I should proceed? I used these commands but it didn’t work.
let me know if i missed anything

Thank you so much in advance

[Nicholas_Bokulich]

Hi @Dani,
It sounds like maybe this tutorial is what you are looking for:

Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)

Creating a TSV BIOM table The following is based on a post by @gregcaporaso. $ qiime tools export table.qza --output-dir ./ $ biom convert -i feature-table.biom -o feature-table.tsv --to-tsv $ biom head -i feature-table.tsv # Constructed from biom file #OTU ID L1S105 L1S140 L1S208 L1S257 L1S281 4b5eeb300368260019c1fbc7a3c718fc 2222.0 0.0 0.0 0.0 0.0 fe30ff0f71a38a39cf1717ec2be3a2fc 5.0 0.0 0.0 0.0 0.0 d29fe3c70564fc0f69f2c03e0d1e5561 0.0 0.0 0.0 0.0 0.0 868528ca947bc57b69ffdf83e6b73bae 0.0 227…

Please take a look at follow the commands given there (note some might be out of date given the age of that post). If you run into any errors please report the full error message here and we will see if we can help.

[Dani (Daniele)]

Hi!! Thank you so much. I`ll try it! And let you know.