OccuPeak

OccuPeak is a peak-calling algorithm designed for ChIP-seq data analysis, which aims to identify transcription factor binding or histone modification sites. Unlike other peak-calling algorithms, OccuPeak does not require an input control dataset to account for local sequencing and GC bias. Instead, it models the background read distribution using the abundant low frequency tags present in each ChIP-seq dataset. The measure of peak significance in OccuPeak, the excess ratio, is only dependent on the tag density of a peak and the global noise levels. OccuPeak outperformed commonly used peak-calling applications in enhancer identification and transcription factor occupation tests and is straightforward and user-friendly to use.