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partial methylation/intermediate methylation
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4.6 years ago
lancelothk • 0
United States

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.

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9 months ago
Freiburg, Germany

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.

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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.

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Yeah, it's both charming and under appreciated.

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10 months ago
Cambridge, MA

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.

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