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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 in map to adjacent RNA-coordinates within 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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Reads can naturally overlap one or multiple adjacent exonic segments , i.e. to edges such that . To this end we extend E by corresponding super-edges se conflating the attributes of atomary exon segments, and apply Definition 2 without loss of generality. 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). |
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