Intersecting Roadmap's Histone ChIP-seq data using BedTools?!?!??!
0
0
Entering edit mode
2.4 years ago

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 • 416 views
ADD COMMENT

Login before adding your answer.

Traffic: 1748 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6