Hi everyone,

I'm trying to annotate ChIP-seq peaks on a reference genome. I'm using R studio and in particular ChIPpeakAnno package.

I read on the user guide that it is possible to annotate peaks using different output parameters (nearestLocation, overlapping, shortestDistance, both, upstream&inside, inside&downstream, upstream, downstream, upstreamORdownstream, nearestBiDirectionalPromoters) with the command annotatePeakinBatch.

I'm annotating peaks with respect to genes and I tried two different outputs, nearest location and shortest distance. In the first case I got the same numer of peaks while instead in the latter case one peak has been associated to different genes.

So I was wondering which is the correct output to be considered for my peak annotation?

Thank you for your help