What is unifrac's input format?

[fluhus (Amit Lavon)]

Hi QIIMErs,

I would like to use QIIME's unifrac functionality. The documentation for --i-table says FeatureTable but I am not sure what that means.

I have a sample*species abundance table in TSV format. How can I use QIIME's unifrac on it?

[colinbrislawn (Colin J Brislawn)]

Hello Amit,

@fluhus

I have a sample*species abundance table in TSV format. How can I use QIIME's unifrac on it?

So, Qiime2 does not use the flat text files common to POSIX programs. Instead, data is imported into 'artifacts' with specific 'semantic types,' listed here. Here's how to import your feature-table-data into a .qza file: Importing data — QIIME 2 2021.8.0 documentation

After importing, you should be ready to use that plugin. Let us know if you have any other questions about this process.

[fluhus (Amit Lavon)]

Thank you, @colinbrislawn! That helps.

In the Importing Data page I only see a conversion to FeatureTable from BIOM format. Does that mean I have to convert my TSV to BIOM and then to FeatureTable? If so, is there a convenient utility for that?

[thermokarst]

@fluhus

is there a convenient utility for that?

Yes, there is a biom command line tool included in your QIIME 2 environment, you can run biom --help for more details.

[fluhus (Amit Lavon)]

That's great, thank you @thermokarst!!