PeakSeq pipeline

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



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  • person_outline Mark Gerstein <>
  • person_outline Joel Rozowsky <>

Publication for PeakSeq

PeakSeq citation

PMCID: 4845000

[…] to the reference human genome (build hg19) using bowtie247, with a maximum mismatch of 2 bases. the alignment rate was >95% for all samples. we identified regions of significant enrichment using peakseq v1.148 using input as background control, tag extension of 200 bp, and a target false discovery rate (q value) of 0.01. the number of peaks obtained for each sample are outlined […]

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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