What is the difference between score and confidence.

[WUD2018]

Dear developer,

I noted the final prediction results have PhaMerScore\PhaMerConfidence\PhaGCNScore\CHERRYScore, which examines the identity, taxa, host of phage-like sequences. My question is, if I filter the results, what threshold you may suggest for these modules?

Thanks.
D.W

[WUD2018]

By the way, I have run the --task contamination. If I would like to select the prophage, should I pay attention to the contamination value (seems like a percentage)? Or just take the Yes/No results. Thanks

[KennthShang]

Hi @WUD2018 ,

I suppose you can directly use the default threshold since they were tested in our benchmark experiments and performed the best. But if you indeed want to use a manual value, maybe 0.75 is a good idea since it is a quartile in statistics.

For the second question, if you only care about the prophage, only check the Yes or No results is enough.

Best,
Jiayu

[WUD2018]

Hi @WUD2018 ,

I suppose you can directly use the default threshold since they were tested in our benchmark experiments and performed the best. But if you indeed want to use a manual value, maybe 0.75 is a good idea since it is a quartile in statistics.

For the second question, if you only care about the prophage, only check the Yes or No results is enough.

Best, Jiayu

Thanks, Jiayu