To perform such analyses, one must use compatible systems of identifiers, reference genomes, gene models, coordinate systems, and so on. For instance, the identification of RNA-editing sites requires that the user have an accurate genotype for the individual as well as RNA-seq reads aligned to that genotype, and variant calls from a DNA-seq experiment should retain not only information about the alignment software but also the precise version of the genome that was used. Bioconductor software is intended to make it easy and automatic to keep track of such issues. This also helps other analysts to determine whether and how a particular processed data set can be integrated with other data sets.
