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jlw-ecoevo / gRodon2

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GC content #9

Closed jotech closed 4 months ago

jotech commented 1 year ago

Thank you for the gRodon package, which is really very useful for me when analyzing codon usage bias!

I have a question concerning the GC output of predictGrowth. What does it measure exactly? I'm asking because I'm getting different GC estimates compared to genome-wide GC estimation provided by e.g., annotation software like bakta.

Is it the GC content of the highly expressed genes? I couldn't find something in the documentation.

jlw-ecoevo commented 4 months ago

Yes, just genes used for prediction - I would not use in place of genome-wide GC estimates, this is just used for internal diagnostics

jotech commented 4 months ago

Alright, this makes sense; thank you for the clarification!