For a bunch of strains we have Chip-Seq on which we have been calling peaks using SWEMBL. We now want to generate an union peak set and I was wondering if people can shed some insight into this and things I should consider.
Is there a "standardised" way of doing this?
If not, when do you merge peaks together (how many bp overlap) for example if strain 1 has a peak from 1 -20 and strain 2 from 18-30 should we merge this (I think we should) but then how do we make sure we don't get greedy and end up with some massive wide peaks (we have 50+ strains).
Any insights or useful tips/tools/scripts people can recommend for doing this?