I asked your question in google.
One of the answers was the following:
It's a NAR-paper from 2013, read it - it answers most of your questions.
"TrueSight: a new algorithm for splice junction detection using RNA-seq."
Yang Li, Hongmei Li-Byarlay, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma
Nucleic Acids Research, Volume 41, Issue 4, 1 February 2013, Page e51,