Is the Qiime2 feature table compatible with FUNGuild?

[ngonza27 (Natalie Gonzalez)]

Hello everyone,

I’m very new to Qiime2 and any sort of bioinformatics work so I apologize in advance for my lack of understanding.

I’m using Qiime2 to look at diversity of Fungi in environmental DNA samples I’ve processed.

I’ve followed the Moving Picture Tutorials and created feature tables of my data and even used the taxa collapse option to generate a table containing my taxa in column one, and the reads per sample in all other columns.

I exported both tables (as .txt files) hoping to run them in FUNGuild but the files don’t match the required FUNGuild OTU table format (http://www.stbates.org/guilds/download_examples.php/?download_file=otu_table_example.txt). I couldn’t find anything online that helped with my issue so I got to thinking… is the Qiime2 feature table compatible with FUNGuild?

I’ve found papers that used Qiime OTU tables for their input into FUNGuild, but none mentioning Qiime2.

[Nicholas_Bokulich]

Hi @ngonza27,
The example feature table you gave looks a little odd, but I think more or less what is described in this tutorial:

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…

Otherwise you may want to get in touch with the FUNGuild developers to troubleshoot, since they would know their format best.

@ngonza27

I’ve found papers that used Qiime OTU tables for their input into FUNGuild, but none mentioning Qiime2.

Note: qiime 1 used biom format in all but the earliest releases... what you describe (a txt document containing an OTU table) is what became known as "classic" OTU tables in qiime 1. The tutorial link above describes how to make a "classic" OTU table.

Good luck!

[ngonza27 (Natalie Gonzalez)]

Thanks Nicholas,

I will switch over to that discussion then.