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  • Trouble with Adding Taxonomy to biom file

    Greetings all,

    I am currently having trouble with adding my taxonomic information to my Biom file. I am running the biom add-metadata command and my output is a biom file with only OTU labels with no taxa info. Without this I am having trouble running further analysis such as core_diversity etc..

    Thanks in advance, and advise would be greatly appreciated

    James

  • #2
    Are you using biom utility to perform the tasks or scripts from QIIME?
    Bioinformaticscally calm

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    • #3
      Thank you for the quick response.

      I am using phyloseq in R to perform beta diversity and NMDS plots, but am using QIIME scripts for the majority of my analysis (pick_open_reference_otus.py, core_diversity_analyses.py, etc.) I have used QIIME scripts to generate my biom file/otu table

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      • #4
        Originally posted by JamesSeward View Post
        Thank you for the quick response.

        I am using phyloseq in R to perform beta diversity and NMDS plots, but am using QIIME scripts for the majority of my analysis (pick_open_reference_otus.py, core_diversity_analyses.py, etc.) I have used QIIME scripts to generate my biom file/otu table
        I have not worked in the direction you're working. However, I've worked just fine with output from command line biom utility and/or R's biom package (from bioconductor).
        Bioinformaticscally calm

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