Figure 1.

Overview of Bisulfighter. (a) mC calling. Bisulfite-converted reads are aligned to a reference genome, and the mC level is estimated as a ratio of C–C matches. A major feature is the utilization of alignment probability for filtering out unreliable alignments, and for weighting mC level estimates. (b) DMR detection. Neighbor cytosines differentially methylated between paired samples are grouped as a DMR (UP or DOWN). A novel HMM-based framework enables automatic learning of chaining criteria, and detection of DMRs using likelihood ratio scores. Colors in the state transition track correspond to those in the state transition diagram at the top. NoCh: no change of methylation between paired samples.