Question: Genome Music for Enhancers and binding sites
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gravatar for anshupa.vssut
12 months ago by
anshupa.vssut20 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 • 388 views
ADD COMMENTlink modified 12 months ago by Chris Miller18k • written 12 months ago by anshupa.vssut20
1
gravatar for Chris Miller
12 months ago by
Chris Miller18k
Washington University in St. Louis, MO
Chris Miller18k 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 COMMENTlink written 12 months ago by Chris Miller18k

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

ADD REPLYlink written 10 months ago by anshupa.vssut20

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 REPLYlink written 10 months ago by Chris Miller18k
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