WGBS vs ONT, which one should I trust? First of all let me apologize if this is not the place for this question. While it can be quite broad, I will try to make it as specific as I can.
Context
I am testing the correlation between Whole Genome Bisulfite Sequencing and Oxford Nanopore methylation calls for one individual (mammal, blood tissue) with replicates at all CpG sites. In the (very) best cases I find a close to 0.9 correlation. Yet, for the part that does not correlate I would like to know which technology is closer to the &quot;biological truth&quot;.
My strategy
My plan would be to first find CpG sites/short CpG regions showing differential methylation states between WGBS and ONT. Then I would validate the methylation states of these sites using a third party technology such as pyromark.
What I am asking to the SE community

First, has anyone done this before ? I would love to hear about your experience

Do you see some critical aspects I should be watching out for ?

Last if you have comments about the strategy I propose here, you are welcome
Methylation can be cell-specific, which makes it difficult to evaluate accuracy on a bulk-cell level (even within the same tissue). How can you tell that the differences you're seeing are due to platform differences, or due to biological variation?
I find that adding more haystacks doesn't help much in working out the truth of a dataset. If you want to investigate biological truth, it would be better to create a biological system with a known methylation (or demethylation) pattern and test that.