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Question: Genome Music for Enhancers and binding sites
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gravatar for anshupa.vssut
2.1 years ago by
anshupa.vssut • 20
anshupa.vssut • 20 wrote:

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 ?
binding sites music enhancer • 653 views
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modified 2.0 years ago by Chris Miller ♦ 20k • written 2.1 years ago by anshupa.vssut • 20
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gravatar for Chris Miller
2.0 years ago by
Chris Miller ♦ 20k
Washington University in St. Louis, MO
Chris Miller ♦ 20k wrote:

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.
ADD COMMENT • link written 2.0 years ago by Chris Miller ♦ 20k

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

ADD REPLY • link written 22 months ago by anshupa.vssut • 20

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.

ADD REPLY • link written 22 months ago by Chris Miller ♦ 20k
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