Examples of (re-)discovered splicing events from single-end split reads. (A) For Drosophila melanogaster, segemehl recovered three different previously described splice junctions linking the minus encoded exon three of MODMDG4 on chromosome 3R to exons on the opposite strand. The strand-reversing splice junctions are annotated between the plus and minus strands. The direction of the strand-reversing splice junctions, i.e. from the minus to the plus strand, was inferred from annotation and prior knowledge. This was necessary because the RNA-seq library used was not strand specific. (B) For the human melanoma transcriptome data set, segemehl identified a very large number of strand-reversing splice junctions in the premelanosome protein (PMEL) gene locus. The split reads that support these junctions split from the plus strand to the minus strand and vice versa. Since we lack additional information, a direction for these junctions cannot be given. Only a selection of strand-reversing PMEL junctions is shown here. (C) For the same data set, segemehl found two alternative transcripts linking CDK2 and RAB5B encoded on human chromosome 12. These junctions (dashed lines) are supported by split reads whose fragments map to the same strand, i.e. split reads that were not strand-reversing. Since the junctions exactly hit the annotated borders of the CDK2 and RAB5B exons, we assigned them to the minus strand. chr, chromosome; PMEL, premelanosome protein.