The output of pb-CpG-tools includes modification probability (column 4) and discretized modification probability (column 9) for each CpG site. I am wondering how should I consider using such information to calculate the average methylation level for each sample? How different they are in terms of representing real methylation rate per site?
Hi,
The output of pb-CpG-tools includes modification probability (column 4) and discretized modification probability (column 9) for each CpG site. I am wondering how should I consider using such information to calculate the average methylation level for each sample? How different they are in terms of representing real methylation rate per site?