peak calling

Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq{{cite journal|last=Meyer|first=Kate D.|author2=Saletore, Yogesh |author3=Zumbo, Paul |author4=Elemento, Olivier |author5=Mason, Christopher E. |author6=Jaffrey, Samie R. |title=Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons|journal=Cell|date=31 May 2012|volume=149|issue=7|pages=1635–1646|doi=10.1016/j.cell.2012.05.003|pmid=22608085|pmc=3383396}} or m6Aseq{{cite journal

|last1=Dominissini |first1=Dan |last2=Moshitch-Moshkovitz |first2=Sharon |last3=Schwartz |first3=Schraga |last4=Salmon-Divon |first4=Mali |last5=Ungar |first5=Lior |last6=Osenberg |first6=Sivan |last7=Cesarkas |first7=Karen |last8=Jacob-Hirsch |first8=Jasmine |last9=Amariglio |first9=Ninette |last10=Kupiec |first10=Martin |last11=Sorek |first11=Rotem |last12=Rechavi |first12=Gideon |title=Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq |journal=Nature |date=28 April 2012 |volume=485 |issue=7397 |pages=201–206 |doi=10.1038/nature11112|pmid=22575960|bibcode=2012Natur.485..201D |s2cid=3517716 }} for detection of post-transcriptional RNA modification sites with software programs, such as exomePeak.{{cite journal|last=Meng|first=J.|author2=Cui, X. |author3=Rao, M. K. |author4=Chen, Y. |author5=Huang, Y. |title=Exome-based analysis for RNA epigenome sequencing data|journal=Bioinformatics|date=14 April 2013|volume=29|issue=12|pages=1565–1567|doi=10.1093/bioinformatics/btt171 |pmid=23589649 |pmc=3673212}} Many of the peak calling tools are optimized for only some kind of assays such as only for transcription-factor ChIP-seq or only for DNase-Seq.{{cite journal |last1=Koohy |first1=Hashem |author2=Down, Thomas A. |author3=Spivakov, Mikhail |author4=Hubbard, Tim |author5=Helmer-Citterich, Manuela |title=A Comparison of Peak Callers Used for DNase-Seq Data |journal=PLOS ONE |date=8 May 2014 |volume=9 |issue=5 |pages=e96303 |doi=10.1371/journal.pone.0096303 |pmid=24810143 |pmc=4014496|bibcode=2014PLoSO...996303K |doi-access=free }} However new generation of peak callers such as DFilter{{cite journal |last1=Kumar |first1=Vibhor |author2=Masafumi Muratani |author3=Nirmala Arul Rayan |author4=Petra Kraus |author5=Thomas Lufkin |author6=Huck Hui Ng |author7=Shyam Prabhakar |date=Jul 2013 |title=Uniform, optimal signal processing of mapped deep-sequencing data |journal=Nature Biotechnology |volume=31 |issue=7 |pages=615–622 |doi=10.1038/nbt.2596 |pmid=23770639 |doi-access=free}} [http://collaborations.gis.a-star.edu.sg/~cmb6/dfilter/] are based on generalized 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. {{cite journal |last1=Wong |first1=Ka-Chun |display-authors=etal|title=SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles |journal=Bioinformatics |date=2014 |volume=31 |issue=1 |pages=17–24 |doi=10.1093/bioinformatics/btu604 |pmid=25192742|doi-access=free }} In the context of ChIP-exo, this process is known as 'peak-pair calling'.{{cite journal |last=Madrigal |first=Pedro |title=Identification of Transcription Factor Binding Sites in ChIP-exo using R/Bioconductor |journal=Epigenesys Bioinformatics Protocols |date=2015 |volume=68 |url=http://www.epigenesys.eu/en/protocols/bio-informatics/1325-identification-of-transcription-factor-binding-sites-in-chip-exo-using-r-bioconductor-prot-68}}

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,{{cite journal|last=Keles|first=Liang|title=Detecting differential binding of transcription factors with ChIP-seq|journal=Bioinformatics|date=26 October 2011|doi=10.1093/bioinformatics/btr605|pmid=22057161|volume=28|issue=1|pages=121–122|pmc=3244766}} MACS2, and MAnorm{{cite journal|last=Waxman|first=Shao|author2=Zhang |author3=Yuan |author4=Orkin |title=MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets|journal=Genome Biology|date=16 March 2012|volume=13|issue=3|doi=10.1186/gb-2012-13-3-r16 |pages=R16 |pmid=22424423 |pmc=3439967 |doi-access=free }} 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,{{cite journal|last=Xu|first=Sung|author2=Wei |author3=Lin |title=An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data|journal=Bioinformatics|date=28 July 2008|volume=24|issue=20|doi=10.1093/bioinformatics/btn402|pages=2344–2349|pmid=18667444|doi-access=free}} ODIN.{{cite journal|last=Allhoff|first=Costa|author2=Sere|author3=Chauvistre|author4=Lin|author5=Zenke|title=Detecting differential peaks in ChIP-seq signals with ODIN|journal=Bioinformatics|date=24 October 2014|volume=30|issue=24|pages=3467–3475|doi=10.1093/bioinformatics/btu722|pmid=25371479}} and THOR. Differential peak calling can also be applied in the context of analyzing RNA-binding protein binding sites.{{cite journal |vauthors=Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J |title=Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo. |journal=EMBO J |year=2016 |pmid=27044921 |doi=10.15252/embj.201593360 |volume=35 |issue=9 |pages=991–1011|pmc=5207318 }}

• ChIP-sequencing
• CLIP-Seq
• DNA Sequencing

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Peak calling

Peak calling

Peak calling

• THOR — http://www.regulatory-genomics.org/THOR

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