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Question: Genome Music for Enhancers and binding sites
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gravatar for anshupa.vssut
4.5 years ago by
anshupa.vssut • 50
Germany
anshupa.vssut • 50 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 • 1.0k views
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modified 4.5 years ago by Chris Miller ♦ 21k • written 4.5 years ago by anshupa.vssut • 50
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gravatar for Chris Miller
4.5 years ago by
Chris Miller ♦ 21k
Washington University in St. Louis, MO
Chris Miller ♦ 21k 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 4.5 years ago by Chris Miller ♦ 21k

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 4.3 years ago by anshupa.vssut • 50

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 4.3 years ago by Chris Miller ♦ 21k
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