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nebiolabs / EM-seq

Tools and Data related to Enzymatic Methylation Sequencing
GNU Affero General Public License v3.0
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Methylation probability #7

Closed olaraym closed 1 year ago

olaraym commented 1 year ago

Hello @bwlang @thuringian @Valiec @PoundKake @tshtatland

Please what is the stipulated cut-off for a CpG position being methylated or unmethylated according to EM_Seq reads?

Thanks.

bwlang commented 1 year ago

Hi @olaraym

In most cases we're looking a reads derived from a population of cells, so there is not one methylation state for all these Cs. If possible, it's best to correlate methylation frequency as a continuous variable with whatever factor you are looking at. If you need the simpler model of 0/1 methylation, you could estimate upper and lower levels by using the lambda and pUC19 control levels within each experiment. Roughly those might be 5% and 95% .

I hope that's helpful...