methylation coverage in the gene region
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2.9 years ago
rthapa ▴ 60

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

methylation • 823 views
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2.9 years ago
ATpoint 65k

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

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