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Sequence correction provided by ONT Research
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Medaka Compatibility with Fungal Reads #494

Closed SueFletcher closed 3 months ago

SueFletcher commented 4 months ago

Hello Thank you for providing this wonderful tool. My question is: Can we use Medaka to analyze reads coming from fungi, or is it only applicable to human data?

cjw85 commented 4 months ago

Medaka is not specialised to human data.

SueFletcher commented 4 months ago

to analyze reads coming from fungi

thank you ,
Can I use it to analyze reads coming from fungi ??

SueFletcher commented 3 months ago

Medaka is not specialised to human data.

Could you please answer my question and tell me if we can use it to analyze reads coming from fungi?

cjw85 commented 3 months ago

I know of no reasons why it could not be used with data from fungi. The inference models used in medaka do not however include data from fungi.

SueFletcher commented 3 months ago

I know of no reasons why it could not be used with data from fungi. The inference models used in medaka do not however include data from fungi.

what's the consequence of the fact that inference models used in medaka do not however include data from fungi please ?

cjw85 commented 3 months ago

The inference models have not been exposed to the nuances of DNA motifs that could be present in fungal genomes during their training process. Our experience is that medaka is typically reasonably robust when extrapolating to these unknown cases; though in principle the models can be less certain in their predictions compared to DNA motifs to which they were exposed in training.