I am currently working with some low resolution (DIP-based, as opposed to chemically-based) methylation data. I would like to employ peak calling to extract methylated regions of high confidence.
I realize that ChIP-Seq peak callers could be used for this, but would prefer one designed for this kind of data. The only software that I am aware of which does this is BALM. Does anyone know of any other good methylation peak calling software that is well-suited for this purpose?