Hi, I know I can use liftover to find syntenic regions between species, but such method is not good for conserved enhancer finding between different cell lines or species. Does anyone have some other good idea?
Do you want to know if the sequence is conserved or the activity is conserved? The way you talk about liftover and syntentic regions makes it sound like you are interested in sequence. But the sequence for any two human cell lines is identical?
If you want to find sequences that are enhancers in two cell lines, you'll have to find some prediction of enhancer activity in those species (like the h3k27ac you mention in the tags) and look at the overlap of peak calls.
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