Simulate Paired-End Bisulfite Read Data

Question

[Chris Miller]

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.

Answer 1

[brentp]

Good question. I looked a while ago; it's not a simple task since methylation has a high spatial autocorrelation and depends on gc-content and position relative to genes (not to mention repetitive elements). Maybe using something from the sequence read archive is the way to go here.

Another option is just to use a normal read simulator--your RMAP or dwgsim from dnaa tools and simulate non-bs-treated reads. Certainly, you should expect those reads to map correctly.

From there, if you know something about the patterns methylation in your genome of choice, you could manually convert some C's to T's (and G's to A's) in your reference with a probability based on what you see in the genome.

And if you build such a tool, please share.

[Chris Miller]

Yeah, I may dig into the RMAP code, see how they did it, and hack something together here in the next few days. If I do, I'll certainly post back here.

Answer 2

[vimal.biochem]

Hi Chris, As I can see this is an old post, I am not sure if such simulator is available. Although simulators like Sherman BSSim DNemulator etc (https://omictools.com/data-simulation-category) are present but I am looking for a tool with C methylation (CG and CH context) and the rate of bisulfite conversion both. As far as i know above-mentioned tools don't address bisulfite conversion. Please suggest me if I am not aware of something already available.