Custom genome use isn't clear

biocore-ntnu / epic2

Ultraperformant reimplementation of SICER

https://doi.org/10.1093/bioinformatics/btz232

MIT License

55 stars 9 forks source link

Custom genome use isn't clear #73

Open c-guzman opened 11 months ago

c-guzman commented 11 months ago

Hey, thanks for the awesome tool, but it isn't very clear what the input to EGF is.

I had originally assumed that EGF has to be between 0-1. But simply providing the effective genome size is also accepted.

Is providing a custom chromosome fasta file + a effective genome size for the EGF parameter correct? Or what is the actual input required? Do you NEED to calculate the fraction before feeding it i to epic? Or will it calculate it for you with some combination of info?

Thanks!

ecroot commented 10 months ago

I would also be interested to learn more about this please

endrebak commented 10 months ago

I will look into this in December when I have a vacation. Can you ping me then? If not, you are likely get good answers by copy-pasting some of the code into GPT4 and asking

DavideBrex commented 10 months ago

I am also interested in this