Hello kind folks,
I have mapped some long-read mouse sequencing to the mouse cDNA sequences.
I now have a list of Ensembl transcripts (e.g. ENSMUST00000232790.2) along with my alignments. How can I use ensembl tools / biomart to determine the "structure" of each transcript, and in particular, the position of the splice junctions relative to the transcript?
I believe this should be possible to do using ensembl tools. I just don't know where to begin.
Best wishes, AJ