Workflows can differ vastly depending on the specific goals of the investigation, but a common pattern is reduction of the data to a defined set of ranges in terms of quantitative and qualitative summaries of the alignments at each of the sites. Examples include detecting coverage peaks or concentrations in chromatin immunoprecipitation–sequencing, counting the number of cDNA fragments that match each transcript or exon (RNA-seq) and calling DNA sequence variants (DNA-seq). Such summaries can be stored in an instance of the class GenomicRanges.
