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Old 06-20-2017, 09:13 AM   #1
JamesSeward
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Default 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
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Old 06-20-2017, 10:19 AM   #2
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Are you using biom utility to perform the tasks or scripts from QIIME?
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Old 06-20-2017, 10:40 AM   #3
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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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Old 06-20-2017, 12:43 PM   #4
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Quote:
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).
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