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jlw-ecoevo / gRodon2

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Question about growth prediction for Eukaryotes #1

Closed susheelbhanu closed 2 years ago

susheelbhanu commented 2 years ago

Hey @jlw-ecoevo,

Firstly, thank you for upgrading gRodon to include estimations for Eukaryotes. Is there an alternate vignette for running the Euks or does one simply use the method established previously (predictGrowth) for the prokaryotes?

Also, will a simple reinstall of gRodon2 suffice or will we need additional scripts?

Thank you very much!

jlw-ecoevo commented 2 years ago

I need to edit the vignette a little but the only real difference is the you should run it with the option mode="eukaryote"

you can find this info by typing ?predcitGrowth to get the helpfile

I also strongly recommend that you include a temperature in your prediction when using eukaryote mode

susheelbhanu commented 2 years ago

Awesome - thank you. And just to clarify, the temperature in this case would be that of the sample environmental conditions, right?!

jlw-ecoevo commented 2 years ago

Yes if you are using metagenomes to get community predictions - if predicting off MAGs or genomes should be your best guess at optimal growth temp (which could also just be conditions under which the organism was samples)

susheelbhanu commented 2 years ago

Got it! Thanks again, Jake.