As an example:
I want to find out where this site in the gene is: Exon/Intron/UTR. How can I do this?
Of course, I can use UCSC Genome Browser for a site. But if I have a huge RNA-Seq data set with these sites and I want the information of their location, how can I automate this? Any tools that you could suggest? Idea is to get a distribution of all the called locations and map them to their genic location.