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biocore-ntnu / epic2

Ultraperformant reimplementation of SICER
https://doi.org/10.1093/bioinformatics/btz232
MIT License
55 stars 9 forks source link

Blacklist region handling #63

Open sitr1014 opened 2 years ago

sitr1014 commented 2 years ago

Hi,

I am curious when I use epic2 to do the peak calling, how does it handle the blacklist regions? Is there a built in/default blacklist filtering or we need to do that saperately after the peak calling?

endrebak commented 2 years ago

There is no blacklist handling. That is best done beforehand by removing reads that overlap the blacklist.