I did not realize that this is a problem. If I do a ChIP-seq using a cancer cell line which harbors numerous translocations and chromosome duplications, how can I map them? Using a non-cancer human reference genome will make the peaks off coordinates. Should I create a reference genome for that cancer cell line?
Or I can still map to the reference genome, and by using whole genome DNA sequencing to identify translocations and duplications. and then move the peaks to the "right" places according to the translocation/duplication information.
Any thoughts on that?