methylation coverage in the gene region

Question

[rthapa]

Hi,

I want to estimate the methylation coverage in the gene region. I have an output file from bismark. I would like to get the methylation coverage ( % of methylated cytosines/total cytosines) in the genomic region. I am not sure if methylpy can handle the output from bismark. Does anyone have suggestion?

Thanks

Answer 1

[ATpoint]

methylKit (R) is an option to conveniently read the methylation calls from bismark. https://bioconductor.org/packages/devel/bioc/vignettes/methylKit/inst/doc/methylKit.html#2_basics