ChIPseeker is a fine annotation tool. Like many of the other tools out there, it identifies the nearest gene based upon the position of the TSS relative to the midpoint of the peak. The reason we are not currently using it in our pipeline is two-fold: 1) being R based it is slower than the methods we have chosen and 2) has difficulties with certain data sets which is not optimal for inclusion in a pipeline. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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