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Gaius-Augustus / TSEBRA

TSEBRA: Transcript Selector for BRAKER
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detailed document for the configure setting #8

Closed sotuamax closed 2 years ago

sotuamax commented 3 years ago

Hi,

I was wondering if there is a detailed document to clarify each argument and its function in the configure file. It is hard to understand what the setting means in your default file.

Many thanks.

Meiyuan

LarsGab commented 3 years ago

Hi,

I added some more information to the 'Configuration File' section of the readme file. For more detailed information about the configuration and the workflow of TSEBRA I would recommend reading the section 'Implementation' of our paper.

I hope this helps. Best, Lars

conchoecia commented 3 years ago

Something simple like this on the README.md would be helpful!

P = protein hints
E = RNA-seq hints
C = ?
M = ?
LarsGab commented 3 years ago

Hi, thanks for the suggestion. I will add such a section for the hint sources of BRAKER to the Documentation. Until then:

E = RNA-seq hints
M = manual hints, BRAKER requires that these hints are used.
C = protein hints from proteins with a 'high' spliced alignment score.
P = protein hints from proteins that have a 'good' spliced alignment score, 
     but that is lower than the score from the ones in 'C'.

Best, Lars

LarsGab commented 2 years ago

I am closing this topic as the documentation has been changed accordingly.

conchoecia commented 2 years ago

Thanks for the update, @LarsGab!