I am using currently using Bismark to align bisulfite-treated reads to the soybean genome. After running the methylation_extractor script on some of my samples it is saying that 80-90% of cytosines are methylated in CpG, CHG and CHH contexts. There is very little difference in methylation % between contexts. Has anyone else experience these high levels of methylation when using Bismark?
I am hoping that is is something with my analysis pipeline and not actually incomplete bisulfite conversion. I did not spike my samples with anything before bisulfite conversion so am unable to test this against a control. Samples that were not converted all show 99.7+% conversion.