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.
