Importing an xlxs file to QIIME2

Hello,

I want to analyze an OTU table in an excel file (xlxs file format). Is there a possibility in https://cancer.usegalaxy.org/ to import it and then rarefy the data and analyze its alpha and beta diversity?

I tried to convert it to a BIOM file but it didn't work.

Thank you in advance,
Brigitta Tissera

Hello again @Brigitta1,

Yes, but it's a bit complicated. It would attempt this starting from the command line, then try to move it into Galaxy later.

First, Save your OTU table as a tsv file. (Excel supports this, though some fixing may be needed!)

Second, convert your .tsv file into a .biom file
https://biom-format.org/documentation/biom_conversion.html#special-case-usage-examples

Third, import this .biom file as a Feature Table into a .qza file
https://docs.qiime2.org/2024.5/tutorials/importing/#feature-table-data

That table.qza file should now be ready to use with Qiime2, including on Galaxy.

Let us know if you have questions!


P.S. I recommend starting from raw data so that everything done to the data will be tracked in the Qiime2 provenance. If you start with Excel, everything that happened before Excel will be lost! :fire:

4 Likes

Thank you so much @colinbrislawn

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