PeakSeq

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PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls

PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.

Citation

Rozowsky J, Euskirchen G, Auerbach R, Zhang Z, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein M

Nature Biotechnology 27, 66 - 75 (2009).

Software download

PeakSeq1.1: Re-coded from scratch, runs slightly faster and it is easier to use.

Refer to the README file in the archive for help on running PeakSeq. In addition, [ these slides] may be helpful.

PeakSeq1.01: Original PeakSeq code.

Additional Resources Related to PeakSeq

Yale Chip-seq Data Pipeline

Software download

Illumina pipeline (wrapper for Illumina pipeline)

Chip-seq scoring pipeline (runs PeakSeq)

Also, one might want to consider ChipSeqSim : http://papers.gersteinlab.org/papers/chip-seq-simu/

Contact

Joel Rozowsky at joel DOT rozowsky AT yale DOT edu or Arif Harmanci at Arif DOT Harmanci AT yale DOT edu.

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