Schematic diagrams of the 4 forms of BS reads, mapping and post processing. 2A. BS reads may be in one of the 4 forms: +FW, +RC, -FW, -RC. 2B. Bowtie aligns C/T converted reads to the C/T converted strands. During the post processing, the number of mismatches is counted except those between read Ts and genomic Cs. Low-quality mappings with many mismatches are removed.