Is there an easy way to convert genomic coordinate to mRNA (transcript) coordinate (with no intronic region) ?
I managed to convert genomic coordinate to gene coordinate (with intron) but i would like to find the coordinate on mRNA.
I have genomic coordinate of iCLIP data.
I want the coordinate of this proteine at the transcript level. I know that transcript are spliced and I want the coordinate on every transcript if the binding site doesn't occure in intron.
These may not be the most lightweight or purpose built, and only may work on certain organisms
I think the reason for not having such a purpose built tool is that it can be a complex task given the nature of things like overlapping genes or similar phenomenon, so VEP and other tools make best-attempt efforts to report all possible results
What are you looking to obtain? As you point out a transcript is built from several different genomic coordinates, not just one.