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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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MEGAN6 biom duplicate id error - way to generate random id from an existing biom table #714

Closed fconstancias closed 8 years ago

fconstancias commented 8 years ago

Hello,

I would like to analyse the "Functional table" from Megan6 with phyloseq R-package. I am able to export the Kegg functional table in biom format from Megan6, but the id is the K0 and depending on the dataset some K0 are shared among different pathways and thus there are a duplicate id error. Is there any easy way to generate random id?

Thanks a lot.

Cheers

screen shot 2016-10-10 at 8 54 24 pm screen shot 2016-10-10 at 8 54 53 pm
wasade commented 8 years ago

As you've indicated, the table is not a validly formatted BIOM table, and as a result, the tools in this repository are not going to be able to parse it. I recommend contacting the developers of the software which produced the table.

Note: with PICRUSt, the strategy is to describe the different pathways a KO belongs too in the metadata.