Is it better to find distance from peaks to genes or distance from summits of peaks to genes?

Question

[mary99]

I am trying to find closest genes to my chip-seq peaks with bedtools closest. You may know that if peak and gene have overlap the distance would be zero. So it means that this computation depends on the length of peaks. Since the MAX and MIN length of my peaks are in far range, I was wondering which would be more precise? Computing distance from total length of peaks or summits of peaks to genes? I know that the summit is center of peaks but I am not sure that summit is exact location of TF binding sites.

Thanks for any discussion.

Answer 1

[Shicheng Guo]

Summits of peaks would be preferred. Actually, the resolution of your analysis would be perfect if it can be controlled within 100-500bp. Do not hope it can be very accurate. if you want to make sure the accurate location for a specific gene, you need to do further precise experiments.

Answer 2

[TriS]

It depends from what you are looking for.

The help page for bedtools will probably answer your question (or part of it)