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Question: phyloseq biom json format conversion needed to hdf5 format for qiime
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gravatar for newmanss
12 months ago by
newmanss0
United States
newmanss0 wrote:

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

ADD COMMENTlink modified 12 months ago by Bernd Fischer540 • written 12 months ago by newmanss0
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gravatar for Bernd Fischer
12 months ago by
Bernd Fischer540
Germany / Heidelberg / DKFZ
Bernd Fischer540 wrote:

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 

 

ADD COMMENTlink modified 12 months ago • written 12 months ago by Bernd Fischer540
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