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Old 08-06-2015, 10:16 AM   #1
biostarx
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Location: Massachusetts

Join Date: Mar 2013
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Post How to combine taxonomy with functions using MEGAN?

Hi SEQanswer community,

I am trying to combine the two different views of Taxonomy and Functional (KEGG and SEED) annotation using MEGAN. I followed the suggestion provided here by Mina. However, the size of my metagenomes is making a tedious task to get the Taxonomy (i.e., "read_id,taxa-path") and Function (i.e., "KEGG/SEED-path, read(s)_id") using Mina's suggestion and then combine those two gigantic files by their read_id with Python.

So, I wondering if someone has a different approach to link the taxa and functional profiles. For example, I'd like to know the taxa distribution within the carbohydrate metabolism (KEGG->Metabolism->Carbohydrate Metabolism). I really appreciate any comment(s) or suggestion(s)!

Thanks,
--
Will
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Old 08-27-2015, 09:03 PM   #2
Polecat
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Location: Australia

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I too would like to know how to do this, so any answers are helpful.
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