Hi All,
I am currently working on viral genome analysis, specifically focusing on HIV. I am using CIRI2 for the identification of circular RNAs and back-splicing junctions.
While analyzing the results, I came across a point of confusion that I hope you could help clarify. For instance, in one of the detected circular RNAs, the back-splicing junction is reported from position 626 to 780. However, the aligned reads supporting this junction extend beyond position 780—for example, up to position 783.
I am trying to understand why the back-splicing junction ends at 780 rather than the actual end of the read (e.g., 783). Is there a specific reason CIRI2 defines the junction endpoint a few bases earlier?
I would greatly appreciate your insights on this matter.
Thank you very much for your time and support.
