This may be a simple question but as far as I can tell the current tools don't quite do this. We have been using target RNA-seq to test the Junction abundance of certain genes, sadly due to probe limitations we were only able to do the junctions, very little of the exons are read and this causes difficult for many annotating tools (or I'm not using them correctly).
Basically all I want to do is take my genome coordinates from my alignment (STAR-2pass) and then annotate them as junctions (not transcripts). i.e. 1-2 or 1-3 exon junctions etc. Are there any tools out there that people know of that will annotate all the unique reads to exons they are contained in?
If not I will have to write some script for this, which will take me some time, and my be useful (limited) if no tools exists currently.