mothur

Use QIIME 2 files in mothur?


#1

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!


#2

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

pat


#3

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?


#4

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


#5

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