UC Riverside

Various techniques are available to profile DNA methylation, either genome‐wide or targeted at specific regions, such as CpG islands and gene promoters. In general, these techniques are divided into two categories: enrichment based and bisulfite conversion based methods. DNA methylation has been associated with gene expression, imprinting, transposon silencing, X‐chromosome inactivation, embryonic development, and cancer. Bisulfite‐conversion‐based methods involve the following three steps: chemical conversion of non‐methylated cytosines to uracils by treating DNA with sodium bisulfite; PCR amplification, and sequencing size‐selected DNA fragments. Sequencing errors, adapter contamination, end‐repair, and single‐nucleotide polymorphisms (SNPs) may affect erroneous methylation calls. Two common major performance measurements of an aligner for BS‐reads are mapping accuracy and methylation call accuracy. Both local alignment and alignment with indels are needed in order to map the reads with sequencing errors, adapter contamination, SNPs, and indels. The number of correctly identified methylation statuses for cytosines is counted only for the cytosines having sufficient read coverage.