PeakSeq
From GersteinInfo
Contents |
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.
