Bisulfite-seq is the standard method for detecting DNA methylation (both 5-methylcytosine - 5mc, & 5-hydroxymethylcytosine - 5hmc) with base level resolution. Bisulfite-seq samples are treated with sodium bisulfite deaminases which deaminates unmethylated cytosines to uracil but methylated cytosines remain unchanged. The uracil (cytosine converted) bases are interpretted as thyamine during sequencing. Bisulfite conversion cannot distinguish between either 5mc or 5-hydroxymethylcytosine (5hmc). Therefore the Bisulfite-seq datasets provide data on the location and abundance of both cytosine modifications.
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