Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??!

Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??!

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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?

GSM958157_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27ac.skin03.bed

And actually, my MAIN question is:

  1. 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!! :’)


Histone


Enhancer


H3K27ac


Epigenetic


BedTools

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