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.
PeakSeq is described in Rozowsky et al. Nature Biotech 27: 66 (more)
PeakSeq version 1.1: Re-coded from scratch, runs slightly faster and it is easier to use, and supports multiple mapped read file formats. Refer to the README file in the archive for help on running PeakSeq. In addition, these slides may be helpful.
PeakSeq version 1.01: Original PeakSeq code.
Additional Resources Related to PeakSeq
Mapability maps for several organisms can be found here
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/
Joel Rozowsky at joel DOT rozowsky AT yale DOT edu or Arif Harmanci at Arif DOT Harmanci AT yale DOT edu.