From GersteinInfo

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.