Distance Between Peaks in Macs Peak-calling data

Question

[saamar.rajput]

I have run Macs Peak-calling for different time points on yeast data sets. Now I want to know the distance between the neighboring peaks in a file for each time point ( There are a number of peaks in each file and I want to know the distance between each neighboring peak). Using some tool in Linux or maybe R.

Answer 1

[Alternative]

Bedtools should do the job for you: http://bedtools.readthedocs.org/en/latest/

Check for "bedtools spacing" or "bedtools closest with -d and -io options".