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Fig. 1
Classification of chimeric reads. (A) Types of nonoverlapping chimeras that may be formed by proximity ligation. The RNA fragments, shown as green and blue arrows, can originate from the same transcript (as shown in the figure) or from distinct transcripts (not shown). The dotted lines in the upper panel indicate ligation sites. (B) Diagram of an overlapping chimera. The RNA fragments originate from two distinct copies of a transcript but are mapped to the same region of the reference gene. (C, top) Examples of nonoverlapping and overlapping chimeric reads mapped to a reference gene. (Bottom) Distribution of the calculated overlap score (L) in all simulated chimeras, simulated nonoverlapping chimeras, and simulated overlapping chimeras.