Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Genome Music for Enhancers and binding sites
0
gravatar for anshupa.vssut
2.6 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 • 743 views
ADD COMMENT • link •
modified 2.5 years ago by Chris Miller ♦ 20k • written 2.6 years ago by anshupa.vssut • 50
1
gravatar for Chris Miller
2.5 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 2.5 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 2.4 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 2.4 years ago by Chris Miller ♦ 20k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1733 users visited in the last hour