ChIPseek allows user to compare two sets of peaks.
In section of "ENCODE", user can also compare:
The output of two dataset comparison includes a Venn diagram, unique peaks in each dataset (i.e. dataset A unique and dataset B unique) and overlapped peaks. All these unique and overlapping peaks can be downloaded in the text format. For these overlapped peak pairs, the relative position of the two peaks is also indicated in the table. Meanwhile, ChIPseek also provides links to UCSC genome browser showing the region of interested peak.*Currently, comparison between the datasets and ENCODE supports human genome assemblies (hg17, hg18 and hg19) only.