This vignette introduces the use of the Bioconductor package DSS (Dispersion Shrinkage for Sequencing data), which is designed for differential analysis based on high-throughput sequencing data. It performs differential expression analyses for RNA-seq, and differential methylation analyses for bisulfite sequencing (BS-seq) data. The core of DSS is a procedure based on Bayesian hierarchical mode...

Bisulfite genomic sequencing is the method of choice for the generation of methylation maps with single-base resolution. The method is based on the selective deamination of cytosine to uracil by treatment with bisulfite and the sequencing of subsequently generated PCR products. In contrast to cytosine, 5-methylcytosine does not react with bisulfite and can therefore be distinguished. In order t...

Bisulfite genomic sequencing is the most widely used technique to analyze the 5-methylation of cytosines, the prevalent covalent DNA modification in mammals. The process is based on the selective transformation of unmethylated cytosines to uridines. Then, the investigated genomic regions are PCR amplified, subcloned and sequenced. During sequencing, the initially unmethylated cytosines are dete...

Labeling chemically for a "single" result: A one-step, nonenzymatic 5hmC thiolation method mediated by bisulfite is highlighted. The 5hmC base can be chemically labeled in single-stranded DNA and detected by using nanopore sequencing.