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Is it still possible to convert .biom tables from QIIME to QIIME’s "classic" OTU table format to use with Explicet? I've tried running the command from biom-format.org

biom convert -i table.biom -o table.from_biom_w_taxonomy.txt --to-tsv --header-key taxonomy

but gives back an error:

biom convert: error: no such option: --to-tsv

Any ideas?

nmshahir
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  • What version of biom are you using? – El Developer Dec 16 '14 at 22:52
  • Sorry for the delay! I honestly don't know which version is installed on our cluster. I'm assuming it's the most recent one. That being said, I've figured out the problem! I should have been using 'biom convert -i input.biom -o output.txt -b --header-key taxonomy' – nmshahir Jan 08 '15 at 16:42
  • try doing: `biom show-install-info` the version number should be at the bottom. The reason why you are getting this error is likely because you have an older version of biom and you need to update it. – El Developer Jan 09 '15 at 17:01

1 Answers1

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I'm using QIIME too and went through the tutorial from Wernerlab. Here I've successfully converted a .biom table into a text file, also with the biom convert command. Maybe you can find clarification in the command line there: 

biom convert -i otu_table.biom -o otu_table_tabseparated.txt -b --header-key="taxonomy" --output-metadata-id="Consensus Lineage"

Cheers, Dennis

Nuss9
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