text: Bisulfite sequencing relies on the conversion of every single unmethylated cytosine residue to uracil. If conversion is incomplete, the subsequent analysis will incorrectly interpret the unconverted unmethylated cytosines as methylated cytosines, resulting in false positive results for methylation. Only cytosines in single-stranded DNA are susceptible to attack by bisulfite, therefore denaturation of the DNA undergoing analysis is critical. It is important to ensure that reaction parameters such as temperature and salt concentration are suitable to maintain the DNA in a single-stranded conformation and allow for complete conversion. Embedding the DNA in agarose gel has been reported to improve the rate of conversion by keeping strands of DNA physically separate. Incomplete conversion rates can be estimated and adjusted-for after sequencing by including an internal control in the sequencing library, such as lambda phage DNA (which is known to be unmethylated) or by aligning bisulfite sequencing reads to a known unmethylated region in the organism, such as the chloroplast genome.