Normalization of BS-seq data between different batches

Question

[Shicheng Guo]

Which method is most suitable for normalization to BS-seq data between different batches? Is it necessary to do it because each value has been calculated by mCG/umCG in each files?

Answer 1

[Devon Ryan]

I assume you're using the raw methylated-CpG and unmethlyated-CpG counts, in which case you can just enter batch into your GLM. If you're actually using a ratio then I haven't a clue how you intend to analyse the results in the first place.