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Protocols

PeakSplitter specifications

Information


Unique identifier OMICS_23187
Name PeakSplitter
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A single peak file and a feature annotation file.
Input format BED+WIG
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Java
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Mali Salmon-Divon
  • person_outline Paul Bertone

Additional information


https://www.ebi.ac.uk/research/bertone/software

Publication for PeakSplitter

PeakSplitter citations

 (24)
library_books

HCFC2 is needed for IRF1 and IRF2 dependent Tlr3 transcription and for survival during viral infections

2017
PMCID: 5679162
PMID: 28970238
DOI: 10.1084/jem.20161630

[…] reads without duplicates using MACS () with parameters “-p 1e-5 --gsize mm --nomodel True --wig --space=10” and relevant input chromatin samples as control data. MACS peaks were then subdivided using PeakSplitter with a valley cutoff of 0.7 and were later filtered for summit height >6. To construct a master peak list from the four MEF samples (two Hcfc2−/− and two WT), the peaks obtained after Pea […]

library_books

Mutant p53 shapes the enhancer landscape of cancer cells in response to chronic immune signaling

2017
Nat Commun
PMCID: 5622043
PMID: 28963538
DOI: 10.1038/s41467-017-01117-y

[…] th the corresponding inputs. For p53 R273H peak calling, p53-enriched regions were first generated by HOMER in comparison to corresponding inputs. The resulting regions were split into subpeaks using PeakSplitter (http://www.ebi.ac.uk/research/bertone/software). For the identification of mutp53 and p65 peak colocalization, p65 peaks were first divided into two groups with and without uninduced mut […]

library_books

Exposure to the widely used herbicide atrazine results in deregulation of global tissue specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice

2016
Nucleic Acids Res
PMCID: 5175363
PMID: 27655631
DOI: 10.1093/nar/gkw840

[…] replicate samples, including corresponding input, shift-size window 73 bp, no model, with P-value threshold <10E−5. The peak regions determined by MACS were further divided into subpeak regions using PeakSplitter with default parameters (). Two biological replicates were used for ChIP-seq and samples for each condition were analyzed independently. The set of peaks was verified at an irreproducible […]

library_books

Motif oriented high resolution analysis of ChIP seq data reveals the topological order of CTCF and cohesin proteins on DNA

2016
BMC Genomics
PMCID: 4986361
PMID: 27526722
DOI: 10.1186/s12864-016-2940-7

[…] ith identical condition. In these cases, for each comparison, peaks were selected that overlapped with the consensus CTS set. Instead of the summit predictions of MACS2, we used the ones located with PeakSplitter, which was developed to discriminate subpeaks (in case of overlapping peaks) and thus gives more accurate local maxima. The distance of the summits relative to the reference points was es […]

library_books

Formation of a Polycomb Domain in the Absence of Strong Polycomb Response Elements

2016
PLoS Genet
PMCID: 4965088
PMID: 27466807
DOI: 10.1371/journal.pgen.1006200

[…] ng was used to increase sensitivity (—nolambda). In addition, we specified a p-value cutoff of 0.00001 for the output peaks. For in depth analysis of the binding regions, output peaks were split with Peaksplitter v0.1 [] and ~20% (peak height≥ 50) of the split peaks were considered for further analysis to rank them into null, weak and strong binding sites. Sequencing data have been deposited to th […]

call_split

Long Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression

2016
PLoS Genet
PMCID: 4852938
PMID: 27135601
DOI: 10.1371/journal.pgen.1005992
call_split See protocol

[…] rameters and cutoff p < 10−5 []. The signal files generated from MACS were normalized to per million total reads. Broad peaks with multiple peaks were split to accurately determine the peak region by PeakSplitter [], requiring per million reads larger than 1. Peaks generated from PeakSplitter were considered as the binding sites and the centers of peaks were considered as the binding centers. The […]

Citations

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PeakSplitter institution(s)
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
PeakSplitter funding source(s)
Supported by from EMBL and BBSRC grant BBG0156781.

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