I have used online tool of analysis and annotation of ChIP-seq data "chipseek" (http://chipseek.cgu.edu.tw/ published here http://www.biomedcentral.com/1471-2164/15/539).
When I compare two lists of peaks to get VennDiag (ovelapping peaks), I get different results for the same list!
In the example bellow, from the same imported "Pif1_peaks.." list of peaks (.bed), I have a total of 1203 peaks in the 1st comparison A (338+865), however, in the second comparison the total number of peaks is 1245 (747+498) for Pif1_peaks..
In addition, in the original bed file "Pif1_..bed", I have only 1173 peaks!
Is there any explication for this?