That is a high false positive and false negative rate, but not fatally so if we get more coverage in return.
Actually, if we are willing to tradeoff coverage for higher probability of false negative and false positives, bisulfite sequencing might also be on the table again, because you can just run the reaction for shorter which would keep more DNA intact (presumably with some kind of bias that might not be worth the headache).
Actually, if we are willing to tradeoff coverage for higher probability of false negative and false positives, bisulfite sequencing might also be on the table again, because you can just run the reaction for shorter which would keep more DNA intact (presumably with some kind of bias that might not be worth the headache).