I know that the methylation level of each CpG site from the TCGA Illumina 450k is illustrated in "beta-value". And the methylation level of each gene will be the average of all the CpG sites' methylation values which have a correlation to that gene. But how can we calculate the value, or the status of methylation from NGS techniques, for examples, MeDIP-chip, MeDIP-Seq or MethylCap-Seq? Do they also use "beta-value" as the parameter of methylation status?

Thank you