I was thinking on how to check for fusion events with an known position using RNA-Seq data. I know that I have several fusion events at different position with a specific exon. I put a figure to explain easily. So there are three different fusion point (green, yellow and pink) with exon1 of the gene. I know the exon sequence but how to check for the fusion point ? I was thinking on first align locally the reads on the exon sequence, to extract these reads, to remove the part that align on the exon sequence and to align them against the whole genome to find the position of the different fusion. What do you think ?