Genome Music for Enhancers and binding sites

Question

[anshupa.vssut]

I am analyzing the relevance of DNA mutations at insulated neighborhood boundaries (i.e CTCF binding sites involved in chromatin looping). Can I use MUSiC for enhancers regions and CTCF binding sites ?

Answer 1

[Chris Miller]

MuSiC's SMG test is just, at it's heart, a test of enrichment of mutations over specific genomic intervals. If you prepare your inputs appropriately, yes, it could be used for any such test.

[anshupa.vssut]

In that case what is the format for my ROI file?how should I supply the co-ordinates of non-coding regions?

[Chris Miller]

That is entirely up to you. It might be as simple as windows tiled across the genome, or more complex by pulling in information from sources like ENCODE.