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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. These areas are those where a protein interacts with DNA. When the protein is a transcription factor, the enriched area is its transcription factor binding site (TFBS). Popular software programs include MACS. Wilbanks and colleagues  is a survey of the ChIP-seq peak callers, and Bailey et al. is a description of practical guidelines for peak calling in ChIP-seq data.
Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq  or m6Aseq  for detection of post-transcriptional RNA modification sites with software programs, such as exomePeak. 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. However new generation of peak callers such as DFilter 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 is about identifying significant differences in two ChIP-seq signals. One can distinguish between one-stage and two-stage differential peak callers. One stage differential peak callers work in two phases: first, call peaks on individual ChIP-seq signals and second, combine individual signals and apply statistical tests to estimate differential peaks. DBChIP and MAnorm are examples for one stage differential peak callers.
Two stage differential peak callers segment two ChIP-seq signals and identify differential peaks in one step. They take advantage of signal segmentation approaches such as Hidden Markov Models. Examples for two-stage differential peak callers are ChIPDiff and ODIN.
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- Koohy, Hashem; Down, Thomas A.; Spivakov, Mikhail; Hubbard, Tim; Helmer-Citterich, Manuela (8 May 2014). "A Comparison of Peak Callers Used for DNase-Seq Data". PLoS ONE 9 (5): e96303. doi:10.1371/journal.pone.0096303.
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- Keles, Liang (26 October 2011). "Detecting differential binding of transcription factors with ChIP-seq". Bioinformatics. doi:10.1093/bioinformatics/btr605.
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- Xu, Sung; Wei; Lin (28 July 2008). "An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data". Bioinformatics 20 (24). doi:10.1093/bioinformatics/btn402.
- Allhoff, Costa; Sere; Chauvistre; Lin; Zenke (24 October 2014). "Detecting differential peaks in ChIP-seq signals with ODIN". Bioinformatics 30 (24): 3467–3475. doi:10.1093/bioinformatics/btu722.
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