Hotspot is a program for identifying regions of local enrichment of short-read sequence tags mapped to the genome using a binomial distribution model. Regions flagged by the algorithm are called "hotspots." The algorithm utilizes a local background model that automatically normalizes for large regions of elevated tag levels due to, for example, copy number effects. Hotpsot is otherwise able to detect regions of enrichment of highly-variable size, making it applicable to both broad and highly-punctate signals. We have applied it extensively to DNase-seq and ChIP-seq data, including transcription factor (CTCF) and histone modification (H3K4me3, H3K36me3, H3K27me3) data.
Hotspot forms the basis of the SPOT data quality metric.You can download further documentation and code for hotspot here: http://www.uwencode.org/proj/hotspot.