Question: phyloseq biom json format conversion needed to hdf5 format for qiime
0
gravatar for newmanss
2.5 years 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

phyloseq hdf5 qiime biom json • 764 views
ADD COMMENTlink modified 2.5 years ago by Bernd Fischer540 • written 2.5 years ago by newmanss0
Answer: phyloseq biom json format conversion needed to hdf5 format for qiime
0
gravatar for Bernd Fischer
2.5 years 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 2.5 years ago • written 2.5 years ago by Bernd Fischer540
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 121 users visited in the last hour