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Revision as of 03:09, 13 July 2011

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

Mapability maps for several organisms can be found here

Datasets

Raw ChIP-Seq Sequence Data: PolII, STAT-1

Yale Chip-seq Data Pipeline

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.