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To avoid redundancy caused by overlapping exons of alternative transcripts, we employ read mappings to the genome. However, our data structure also permits mappings to de novo transcriptome assemblies providing given that one provides coordinates relative to the contig of the corresponding locus. The annotation mapping algorithm then assigns genomic read mappings to edges of the segment graph, following Definition 2.

Definition 2 (Read Assignment): an a read belongs to an edge  iff all subsequent read positions mapped to the genome  map to adjacent transcript coordinates  within e: .