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One important step in calling methylation of a genome is to map bisulfite reads. Mapping of bisulfite reads is different from that of ChIP-Seq and RNA-Seq data since the non-methylated Cs are converted to Ts by bisulfite treatment and subsequent PCR. The bisulfite reads are difficult to map to the reference genome due to the high number of mismatches between the converted Ts and the original Cs.
(Lim et al., 2012) BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol.