Calculate methylation coverage genome wide

[OceaneMion]

Hi,

I am currently working with Modkit and would like to know if there is a way to extract the global CpG methylation coverage (I am focusing on 5mC) from a bedMethyl file, or how could I calculate this ?

I would like to compare this methylation coverage with the overall genome coverage.

Thank you very much for your help!

[ArtRand]

Hello @OceaneMion,

I apologize about the delay in getting back to you. If you're looking to calculate statistics on the 'valid coverage' at CpG sites. I would use the --cpg flag for modkit pileup. Then filter to rows where the 'name' column (column 4) is m, then calculate your statistics on the 'score' column (column 5).

This list of score values represents the number of reads with base modification calls (modified or unmodified) that are passing the filter criteria. These values will be $\leq$ the read coverage values since reads with a C>D mismatch will not be counted and reads with calls failing the filter criteria will not be counted.

Please let me know if this answers your question.