Hello,
I prepared the tsv file to upload to Galaxy website. However, when I upload the file, it gives error in "Data Format" step.
Here is how my tsv file looks like:
I appreciate any help.
Thank you,
Zahra
Hi @Barandouzi you can easily reformat the data for use in LEfSe via Dokdo.
If you read the dokdo documentation and the tutorials you'll see that dokdo uses the QIIME 2 API.
Here are the installation instructions. Though it is much easier to simply install like this:
conda activate qiime2-amplicon-2024.10
pip install git+https://github.com/sbslee/dokdo
dokdo --help
Then run the prepare-lefse command as described here. This will hopefully minimize any manual file formatting issues. Then upload to Galaxy.
-Mike
1 Like
Thank you So much for your reply.
Zahra