phyloseq biom json format conversion needed to hdf5 format for qiime
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newmanss • 0
@newmanss-7190
Last seen 3.7 years ago
United States

Hi,

I have analyzed my metagenome data with phyloseq and used the R package biom to output a biom file containing my phyloseq normalized and filtered data.  I need to run a statistical test in Qiime.  My biom file generates an error that appears to be a column name problem for 'id'.  As best I can determine, the source of the problem is that my biom file is formatted in the old version 1.4 json, and qiime requires version 2 hdf5 format.  I have repeatedly tried the biom convert command recommended here, http://biom-format.org/documentation/biom_conversion.html.  Can someone please help me with the correct conversion method to convert from the R biom file to a format accepted by qiime?

Susan

biom json hdf5 qiime phyloseq • 1.1k views
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Bernd Fischer ▴ 540
@bernd-fischer-5348
Last seen 4.7 years ago
Germany / Heidelberg / DKFZ

biom is a CRAN package, you should directly write to the respective CRAN mailing list or to the authors of the package.

There exists as well a vignette for the biom package: https://cran.r-project.org/web/packages/biom/vignettes/biom-demo.html 

 

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