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biocore-ntnu / epic2

Ultraperformant reimplementation of SICER
https://doi.org/10.1093/bioinformatics/btz232
MIT License
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effective genome size #47

Open tan5251 opened 3 years ago

tan5251 commented 3 years ago

Hi. I had used the method named "epic-effective" to calculate effective genome size ("https://www.biostars.org/p/185948/). My data is paired-end 150bp and species is Sus. Our final results is 0.9720847535129595. Is it normal? maybe too high??

endrebak commented 3 years ago

For mammals, around 90% is about right.

Changing the setting to eg 85% isn’t going to change much. Also, the order of the results will be the same, but you might get fewer/more regions with a significant FDR.

tan5251 commented 3 years ago

The EGS does not affect the order of results but does affect FDR. Thanks for your reply.