I have a bed file of SNPs and also H3K27ac ChIP-seq .broadpeak file from Roadmap epigenome...
I want to find the SNPs in my list that intersects a H3K27ac peak using BedTools intersect
Is the publicly available .broadpeak already completely processed? (meaning I dont need additional filtering) or should I filter the intervals inside my broadpeak file FURTHER based on its pValue or qValue first?? If so what would be the appropriate cut-off for this type of analysis?