5.6 years ago by
There are lots of ways to do this. I think the easiest solution is to use knowledge of known exon junctions.
1). Providing TopHat with a .gtf file should produce a junctions output file (technically, it already produces this file, but I think it should be empty unless you provide a reference list of transcript locations)
2) Use a software to predict splicing events. This will give you a prioritized list (in addition to providing counts for all relevant splicing junctions). MATS is my favorite tool for this, and MISO is another popular option.
3) If it is relevant, there are also gene fusions programs. I have a slight preference for chimerascan, but I have tried all of the following programs:
I'm sure there are also options for generically splicing the .bed file for split reads, but I would typcially focus on looking for software that also assists with the downstream analysis (for whatever specific application I am interested in). So, I don't really have recommendations on this end.