Entering edit mode
3.0 years ago
ConvolutedGenome
▴
50
Hi all,
I want to prioritise my list of 112 SNPs by looking at those that lie within open chromatin regions and/or active promoter/enhancer histone marks
In order to do that I have downloaded several Histone modification ChIP-seq data from Roadmap epigenomics as a .bed file
But I have trouble understanding the .bed file that I downloaded from GEO.. so can somebody enlighten me as to what the fourth and fifth column are supposed to mean?
And actually, my MAIN question is:
- Will simply intersecting the SNPs and ChIP-seq .bed file using BedTools be sufficient for what I'm trying to answer? I'm not sure... because it seems idk.. to easy? Am I missing something? Is the above .bed file even the correct .bed file to use?
Thank you!! :')