Methods to Study Splicing from RNA-Seq

<p>Graphical representation of methods to study splicing from RNA-Seq. Methods are divided according to whether they perform Mapping, Reconstruction of events or isoforms, Quantification of events and/or isoforms and whether they can perform a Comparison between two or more conditions of event or isoform relative abundances, or of isoform expression. We only list the Mapping methods that are spliced-mappers or the ones that use some heuristics to map to known exon and junctions. Methods for Reconstruction (blue), Quantification (green) and Comparison (red) are divided according to whether they work with isoforms (lighter color) or with events (darker color). Methods that work at both levels, are overlapped by the two color tones. Some methods perform reconstruction and quantification and are grouped with those that only perform reconstruction. Some mapping methods also perform quantification and are repeated in two levels. Methods that require an annotation are indicated. Quantification methods that work with or without annotation are in different groups. Solid arrows connect Mapping methods to the tools in the other three levels; since, in principle, any Mapping method producing BAM as output could be fed to methods reading BAM as input. Some methods perform Mapping and Quantification or Mapping and Differential Splicing, and are connected with a solid arrow too. We indicate with dashed gray arrows those cases when a Comparison method can use the output from a Quantification method.</p>