ChIP-seq and the output of SPP
I found the answer to this question and some more interesting details that people who stumble upon this might also need. First look at this paper, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191340/ and especially this figure, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191340/figure/F3/. The MSER is a ratio of the fraction of discovered peaks to the fraction of the sampled reads to recapitulate them, so if you are able to return all of the peaks with a small sample of reads then you have excellent coverage. Now even though you have great and well defined peaks you need another sample to confirm that they are indeed significant, and you can do this with the IDR, see this website - https://sites.google.com/site/anshulkundaje/projects/idr. The IDR is laid out pretty well in the supplemental material for this ENCODE paper, http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html. Beautiful!!