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I'm working on an ancient DNA project (humans) examining the methylation patterns for a single nuclear gene on chromosome 5. I understand the protocols of bisulfite sequencing, and in general how the methylation is identified from the sequence results, but due the degradation in ancient DNA, some methylated cytosines may become deaminated to thymines, creating a GC->AT conversion. Since bisulfite sequencing allows for all retained C's to be classified as methylated in the original sequence, I'll be underestimating methylation depending on how degraded the samples are. Is there a way to address this?

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