Over at Bitesize Bio, Judith Brouwer offers 10 tips for improving bisulfite sequencing outcomes. "In my experience, depending on the locus of interest (roll up your sleeves for C/G-rich areas), bisulfite sequencing doesn't always give perfect results the first time," she says.
Top on her list is to be sure to design very good primers. "Since you don't know the methylation outcome of your sample beforehand, you need to make sure that primer annealing is not affected by the methylation status of your primer target sequences," Brouwer says.
Other ideas she shares are to use semi-nested PCR and to choose the proper purification method. Additionally, Brouwer suggests using a tool like BiQAnalyzer for analyzing the data.