For single CpG site, what may cause the partial methylation/intermediate methylation in BS-seq data?
What I know are:
1. allelic methylation difference in diploid cell.
2. sequencing/bisulfite error (after trim lower quality bps, filter out low bisulfite conversion rate reads)
3. Inter-cell variation for mix cells sample.
4. inter-cell variation even for a single cell type (Suggested by Devon Ryan)
Is there any thoughts about how to distinguish each type? And is there any literature about this topic?