Question: Bisulfite Sequencing-Bismark: Observing abnormally high methylation levels
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2.0 years ago by
ryanzapotocny0 wrote:

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.

alignment next-gen • 726 views
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