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Definition 2 (Read Assignment): a read belongs to an edge iff each two read positions bases contiguously aligned to the genome are adjacent map to RNA-coordinates in e: . |
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Definition 2 requires the read mapping to comply with the annotated exon-intron structure. Specifically, indels of genomic read mappings are considered in a different manner than split-mappings, and discriminated by the description of the alignment. The definition is further extended to match the attributes of specific RNA-Seq experiments, for instance in the case of stranded protocols. All reads r that fulfill Definition 2 are assigned to their corresponding edges e. |
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