Fig. 5
From: Evaluation of whole-genome DNA methylation sequencing library preparation protocols
Cytosine retention for methylation controls, namely lambda phage (A), pUC19 (B), and mitochondrial DNA (C). Lambda phage and pUC19 are added to the genomic DNA to serve as unmethylated and methylated controls, respectively. Mitochondrial DNA is a good source of unmethylated DNA that can be used in lieu of spike-in controls. Note, PBAT only had one technical replicate, so there is no “Rep. 2” half on these violins. In addition, the mitochondrial DNA required at least three reads covering each CpG, while the spike-in controls required at least one read due to the fewer number of reads relative to the genomic DNA. This coverage requirement can result in all CpGs for a sample being 1.0, such as in Kapa Sample A in B