A major challenge in bisulfite sequencing is the degradation of DNA that takes place concurrently with the conversion. The conditions necessary for complete conversion, such as long incubation times, elevated temperature, and high bisulfite concentration, can lead to the degradation of about 90% of the incubated DNA.
One major obstacle with bisulfite sequencing is that DNA degrades alongside its conversion process. The factors required for complete conversion, such as extended incubation times, elevated temperatures, and high concentrations of bisulfite, can lead to about 90% degradation of the incubated DNA.