I apologise in advance as this may turn out to be extremely simple to solve!
I have one file that contains 200bp coordinates centred upon subpeak summits from MACS. These being in BED3 format.
As i have extended the coordinates +/- 100bp and there are some instances where the new subpeak coordinates overlap. However i want to make them nonoverlapping with the same coverage. I want to extract sequence for the coordinates and i do not want redundant sequence.
Anyone know of a quick method to parse the coordinates and alter then so, for example, the first coordinate would be made to end at the point where it overlaps with another?
I hope this is clear?!