Figure 2.

Schematic overview of RNAnue. Sequence reads are either preprocessed (clipped, trimmed and merged) or directly subjected to split read detection. This includes mapping, calculation of filter scores (e.g. complementarity, hybridization energy) and is followed by the clustering of the identified split reads. Clusters are merged with overlapping annotated genome features to so called transcript interactions. These are evaluated statistically and the p-value together with the global filtering scores is reported in the transcript interaction table.