Use QIIME 2 files in mothur?

I’d really like to do some analyses in mothur that are not available in QIIME 2. However, I would like to use my OTU, taxonomy, and tree files that are already created in QIIME 2. Is there an easy way to do this?

I tried biom.info and make.shared commands in mothur but neither opened with my QIIME 2 biom files. (Are these commands compatible with QIIME 2 biom files? I’m not sure which version of biom files QIIME 2 uses but I do know QIIME 2 biom files differ from QIIME 1 in that they don’t contain taxonomic information…QIIME 2 has a .tsv file for taxonomy + .biom file for the OTU table).

Alternatively, I can convert OTU and taxonomy files to .txt files. Would that work with mothur?

Any thoughts or suggestions are appreciated.

Thanks!

The latest release of mothur (v1.41) should read the current biom standard format.

pat

Hmmm…I’m using v1.41 but get the below error message plus an empty shared file when I use the following code:

biom.info(biom=feature.table.biom)

[ERROR]: you file does not have a type provided.
[ERROR]: you file does not have a matrix_type provided.
[ERROR]: you file does not have a matrix_element_type provided.
[ERROR]: you file does not have a rows provided.
[ERROR]: you file does not have a columns provided.
[ERROR]: you file does not have a shape provided.
[ERROR]: you file does not have a data provided.

QIIME 2 exports biom files in v2.1. The mothur wiki says mothur only reads v1 biom files. Has this been updated in v1.41?

Can you try biom.info(biom=feature.table.biom, format=hdf5)?

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