I'm reading the Tophat manual, and I'm trying to get clarification on what exactly a "coverage island" is. According to the tophat manual:
TopHat generates its database of possible splice junctions from three sources of evidence. The first source is pairings of "coverage islands", which are distinct regions of piled up reads in the initial mapping. Neighboring islands are often spliced together in the transcriptome, so TopHat looks for ways to join these with an intron.
I've done plenty of googling on this terminology, but I don't quite have a solid understanding yet. A visual would be huge. My current understanding is that the reads, being reverse-transcribed from RNA, will sometimes map to non-contiguous sites in the genome as a result of transcript assembly.
Here is a simple drawing of that understanding. What I think represents a coverage island is within the blue circle. Can someone verify or correct my understanding?