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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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Methylation level calculation for PMD #152

Closed juheon closed 4 years ago

juheon commented 4 years ago

I want to make sure how the methylation level of each bin is calculated for PMDs. According to the manual, "The program calculates in nonoverlapping bins the total methylated and unmethylated read counts.". Does it mean "Total number of methylated reads in each bin" / "Total number of reads in each bin"? Or, do you calculate the methylation level of each CpG and calculates the mean of all CpGs in each bin?

bdecato commented 4 years ago

Hi Juheon,

It's the total number of methylated reads in each bin divided by the total coverage of the bin.

Thanks,

Ben

juheon commented 4 years ago

Thank you!

On Thu, Jun 4, 2020 at 3:34 PM Benjamin Decato notifications@github.com wrote:

Closed #152 https://github.com/smithlabcode/methpipe/issues/152.

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