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PeakSeq specifications


Unique identifier OMICS_00453
Name PeakSeq
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment.
Output data A file with peak regions ranked with increasing Q-values.
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Advanced
Version 1.3.1
Stability Stable
Maintained Yes




No version available


  • person_outline Mark Gerstein
  • person_outline Joel Rozowsky

Publication for PeakSeq

PeakSeq citations


Genome wide association analysis of chronic lymphocytic leukaemia, Hodgkin lymphoma and multiple myeloma identifies pleiotropic risk loci

Sci Rep
PMCID: 5253627
PMID: 28112199
DOI: 10.1038/srep41071

[…] s that map to the pathway genes, and determining if any of these SNPs fall within ENCODE peak data, namely DNase-seq peaks of open chromatin, FAIRE peaks of open chromatin, TFBS SPP-based peaks, TFBS PeakSeq-based peaks and Histone peaks. In addition, eQTLs were determined using several eQTL databases, namely eQTL Browser, GTEx and seeQTL. Common networks were identified using GeneMANIA. This data […]


Quantitative analysis of ChIP seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia

PMCID: 5090954
PMID: 27822313
DOI: 10.1186/s13072-016-0090-4

[…] t control, the peak caller FindPeaks (version 4.0) was used. Although alignment tools in general produce comparable results, FindPeaks [] is most sensitive in distinguishing enrichment [] compared to PeakSeq [], USeq [] and MACS [].Identification of enriched regions requires a null distribution [], ideally in the form of a sequenced input sample which allows for proper correction of background ano […]


Complex Patterns of Association between Pleiotropy and Transcription Factor Evolution

Genome Biol Evol
PMCID: 5174740
PMID: 27635052
DOI: 10.1093/gbe/evw228

[…] e ChIP-seq experiments, every experiment was subject to two peak calling procedures (), SPP (which determines peaks based on by the Signal Score ([ChIP signal enrichment]/[input DNA signal])) (), and PeakSeq (which determines peaks based on the expected false discovery rate) (). Data shown is from the SPP peak calls, which were shown to be consistent for peak calling (). This yielded the number of […]


Tissue and Time Specific Expression of Otherwise Identical tRNA Genes

PLoS Genet
PMCID: 4999229
PMID: 27560950
DOI: 10.1371/journal.pgen.1006264

[…] cance of the binding activity for young adult nematode were downloaded from modENCODE (Snyder_N2_POLIII_YA; modENCODE_4034) [,]. The ChIP-seq data generated by this experiment were analyzed using the PeakSeq peak-calling algorithm []. H3K4me3 MA2C scores for young adult nematodes were downloaded from modENCODE (Lieb_N2_H3K4me3_YA; modENCODE_3552); H3K27ac MACS scores for young adult nematodes were […]


Identifying peaks in * seq data using shape information

BMC Bioinformatics
PMCID: 4905608
PMID: 27295177
DOI: 10.1186/s12859-016-1042-5

[…] any different approaches to peak calling have been developed. The density of the ChIP signal can be analysed directly (Findpeaks []) or compared to a control signal (CCAT [], CisGenome [], Erange [], PeakSeq []). Signal processing approaches including Gaussian Kernel Density Estimation (FSeq [], QuEST []), Hotelling filters (DFilter []) and wavelets [] have also been applied to this kind of signal […]


A uniform survey of allele specific binding and expression over 1000 Genomes Project individuals

Nat Commun
PMCID: 4837449
PMID: 27089393
DOI: 10.1038/ncomms11101

[…] verage. Furthermore, significant allele-specific SNVs have a minimum of six reads.For ChIP-seq data, allele-specific SNVs have to be also within peaks. Peak regions are determined by first performing PeakSeq for each of the 14 personal haploid genomes with ChIP-seq data. Only a single read per strand per position is kept and duplicates removed. The fragment length is set to 200 bp. Peak calling is […]


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PeakSeq institution(s)
Molecular Biophysics & Biochemistry Department, Yale University, New Haven, CT, USA; Molecular, Cellular & Developmental Biology Department, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA
PeakSeq funding source(s)
Supported by the NIH.

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