CSV to a qiime2 readable format

User Support
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Hi @coralgal! The biom convert tool requires that files follow some strict formatting guidelines:

  • The file must be in TSV format (i.e. tab-separated values). CSV files, Excel files, etc. won’t work but you can easily convert those file types to TSV (e.g. by exporting from Excel).

  • The first cell in the file must be #OTU ID

  • The first column contains “feature” identifiers (e.g. OTU IDs, Greengenes IDs, ASV IDs, etc.)

  • Each subsequent column contains the abundances of features within a sample. Each column name corresponds to a sample ID.

Here’s an example of a file containing two features (feature1 and feature2) and three samples (sample1, sample2, and sample3):

#OTU ID   sample1  sample2  sample3
feature1      1.0      3.0      0.0
feature2      0.0      1.0      5.0

Can you try formatting your data in this manner and then convert it with biom convert? If you’re having issues after that, feel free to send me your TSV file and I can take a closer look.