Improved algorithm for CpG methylation state determination as implemented in the BISMA software. BISMA detects CpG sites in the reference sequence which is aligned to the experimental sequences. After identification of a guanine at the position aligned to the reference CpG's guanine, the next base in 5' direction is used for determination of the methylation state. Methylation state "unknown" refers to sites lacking clear methylation information due to mutations or sequencing problems.
Rohde et al. BMC Bioinformatics 2010 11:230 doi:10.1186/1471-2105-11-230