I'm looking for a tool that can simulate bisulfite paired-end reads.
RMAP includes a some nice tools that allow you to either simulate paired end reads or bisulfite reads, but not both. It's also got parameters for the rate of CpG methylation, the rate of bisulfite conversion, and mutation rate. Does anyone know of something comparable that will generate this data for bisulfite-treated paired-end reads?
Just trying to avoid reinventing the wheel here.