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To avoid redundancy caused by overlapping exons of alternative transcrip= ts, we employ read mappings to the genome. However, our data structure also= permits mappings to de novo transcriptome assemblies given that o= ne provides coordinates relative to the projected contig of the assembled l= ocus. The annotation mapping algorithm then assigns genomic read mappings t= o edges of the segment graph, following Definition 2.
Definition 2 (Read Assignment): a read belongs to an ed= ge iff each two bases contiguously aligned to the genome&n= bsp; map to adjacent RNA-coordinates within e: .
Definition 2 requires the read mapping to comply with the annotated exon= -intron structure. Specifically, indels of genomic read mappings are consid= ered in a different manner than split-mappings, and discriminated by the de= scription of the alignment. The definition is further extended to match the= attributes of specific RNA-Seq experiments, for instance in the case of st= randed protocols. All reads r that fulfill Definition 2 are assign= ed to their corresponding edges e.
Reads can naturally overlap one or multiple adjacent exonic seg= ments , i.e. to edges such that . To this end we extend E= em> by corresponding super-edges se conflating the attributes of a= tomary exon segments, and apply Definition 2 without loss of genera= lity. Note that in the case of split-mappings, exonic segments represented = by super-edges can be separated by intermediate intronic edges. Paired-end = reads are mapped jointly to super-edges that combine the exonic regions to = which each mate is mapping, which in turn can be already super-edges (Fig.2= ).
Figure 2: mapping reads to the segment graph spanned by the anno= tation. (A) Exon segments and their respective su= per-edges in the case of overlapping exons. (B) Super-edge= s inferred by alternative splice-junctions. (C) Paired-end= mappings to super-edges coalesced by (super-) edges constructed in (A) and= (B).