Mouse metagenome using GMGC or MouseGutCatalog

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ullo...@googlemail.com

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Feb 9, 2021, 1:06:39 PM2/9/21
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Dear Luis,
I'm starting with another mouse project. I just saw that gmgc contains more mouse samples now than the mouse gut catalog from ng-metaprofiler. Would you suggest using the gmgc variant and if so, can I restrict the mapping/annotation to the mouse genes, and does that make sense in your opinion?
There is even a big mouse catalog (871 samples) from HZI Braunschweig, does it make sense to include that at some point in the mouse gut profiler as standard? It includes the data from Xiao et al 2015. They will soon release v2 with even more mice and as far as I know, annotated with eggnog.

Best,
Ulrike

Luis Pedro Coelho

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Feb 21, 2021, 10:03:59 PM2/21/21
to Ulrike Löber, NGLess List
Hi Ulrike,

(Because of the Lunar New Year celebrations, I'm now catching up with a lot of the non-urgent email—and I apologize for marking your emails non-urgent)


I'm starting with another mouse project. I just saw that gmgc contains more mouse samples now than the mouse gut catalog from ng-metaprofiler. Would you suggest using the gmgc variant and if so, can I restrict the mapping/annotation to the mouse genes, and does that make sense in your opinion?

Yes, that makes sense.

There is even a big mouse catalog (871 samples) from HZI Braunschweig, does it make sense to include that at some point in the mouse gut profiler as standard? It includes the data from Xiao et al 2015. They will soon release v2 with even more mice and as far as I know, annotated with eggnog.

You can always do a simple test on 1 or 2 samples and check which variants give you higher mapping rates, otherwise, I don't really know a way to compare (except by intuition, where I guess it's not so much about have MORE samples as having samples closer to yours).

HTH
Luis


Best,
Ulrike


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