Peak calling is a computational method used to identify areas in a genome that have been enriched with aligned reads as a consequence of performing a ChIP-sequencing or MeDIP-seq experiment.
[7] Many of the peak calling tools are optimised for only some kind of assays such as only for transcription-factor ChIP-seq or only for DNase-seq.
[8] However new generation of peak callers such as DFilter[9] are based on generalised optimal theory of detection and has been shown to work for nearly all kinds for tag profile signals from next-gen sequencing data.
It is also possible to do more complex analysis using such tools like combining multiple ChIP-seq signal to detect regulatory sites.
Differential peak calling can also be applied in the context of analyzing RNA-binding protein binding sites.