Accurate Mapping of RNA-Seq Data

Abstract

The mapping of RNA-Seq data on genome is not the same as DNA-Seq data, because the junction reads span two exons and have no identical matches at reference genome. In this chapter, we describe a junction read aligner SpliceMap that is based on an algorithm of “half-read seeding” and “seeding extension.” Four analysis steps are integrated in SpliceMap (half-read mapping, seeding selection, seeding extension and junction search, and paired-end filtering), and all toning parameters of these steps can be editable in a single configuration file. Thus, SpliceMap can be executed by a single command. While we describe the analysis steps of SpliceMap, we illustrate how to choose the parameters according to the research interest and RNA-Seq data quality by an example of human brain RNA-Seq data.