Dear list,

The ChIPsim package is now available in the development version of Bioconductor. It provides a framework for the simulation of ChIP-seq and nucleosome positioning experiments. The package provides functionality that allows a user to supply a model of protein binding sites throughout the genome that is then used to generate sequence reads (with possible sequencing errors) from a supplied reference sequence. The package incorporates a simulation of nucleosome positioning but provides all the infrastructure necessary to adapted the same approach to other types of experiments. This simulation was designed to enable the comparison of ChIP-seq analysis pipelines from read mapping to peak-calling. It may also prove useful for the planning of ChIP-seq experiments.

Please let me know if you have any questions, suggestions, comments or bug reports.

Regards,
Peter

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