Bisulfite libraries are of two distinct types (Chen et al., 2010): in the first scenario the sequencing library is generated in a directional manner, i.e. the actual sequencing reads will correspond to a bisulfite converted version of either the original forward or reverse strand (Lister et al., 2009). In a second scenario, strand specificity is not preserved, which means all four possible bisulfite DNA strands are sequenced at roughly the same frequency (Cokus et al., 2008; Popp et al., 2010).
