Abundance comparison of unprocessed large mitochondrial RNA transcirpt

Question

[caggtaagtat]

Hi there,

In my project, I want to compare the abundance of the unprocessed mtRNA transcript with the help of my RNA-Seq data. In mitochondria, the whole DNA gets transcibed at once. Subsequently, the RNA templates for the singel genes are cut out of that large transcript. To estimate the abundance of the unprocessed mtRNA transcripts, I would like to search for reads covering two neighboring mRNA templates, which are seperated after processing. I already mapped my data with STAR and salmon. Is there a way to access the information about reads overlapping two genes, which probably were excluded because of that? Or do I have to add a new gene to my annotation file for Salmon, which consists of the fused gene sequences?