partial methylation/intermediate methylation

Question

[lancelothk]

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?

Thanks

Answer 1

[Devon Ryan]

I'll add 4. inter-cell variation even for a single cell type. Much of biology is stochastic, why not methylation too?

There's no trivial general method to distinguish each of these. Much of this would require single cell BS-seq, ideally with something like PacBio or ion torrent machines, or simply sequencing either more samples or the same samples again and comparing the results.

[lancelothk]

Thanks for your reply. The stochastic nature of biology is the charming part, right? I am from CS background, just want to get some biological ideas for this topic.

[Devon Ryan]

Yeah, it's both charming and under appreciated.

Answer 2

[Matt Shirley]

5. Mapping ambiguity due to low complexity sequences, though it depends on how you handle these.

6. Mis-mapping due to reference issues such as sequence compression / incomplete assemblies.