Simulation of gene level methylation data

Question

[Mamatha Y S]

I would like to simulate gene level methylation data ..if not the gene level at least I need to simulate CpGs but these for my specific disease for example I want to simulate methylation data for mastitis I need control and disease data with replicates ..how to simulate this is there any package?

I want to simulate methyl count for specific genes for the disease data.

Answer 1

[mark.ziemann]

What type of data do you want to simulate, array or bisulfite seq or enrichment seq? I don't think it is normal to simulate an exact disease, but rather select genes by random and then introduce differential signals in the case group, and then see whether the pipeline can recover those signatures.

[Mamatha Y S]

Thank you so much for your response..I want to simulate WGBS data. Can u please explain how I can do that or is there any paper ?. I have real data can I simulate based on that.

[mark.ziemann]

Let's say you have a real dataset that consists of counts of meth and unmeth cytosine at each CpG site for one sample with overall 30X coverage. One approach could be to upscale this by a factor of 10 and then downsample it back to a realistic coverage n=6 times (n=3 controls and 3 cases), then you can introduce differential methylation in the case datasets at a set number of positions by a set percentage (delta-beta), and also introduce an aspect of random noise (SD). By running trial with variable values of n, delta-beta and SD, you will have a set of fairly realistic counts, which you can use to benchmark WGBS statistical pipelines. If you need the fastq files corresponding to the raw sequence for these counts, you could probably use a tool like Sherman or MethylFASTQ.

[Mamatha Y S]

thank you so much