How to detect genes with read-through in RNA seq analysis

Question

[emurb]

Hello,

I am new with RNA seq, and it is my first real analysis to perform. I have some fastq files in which I know I have genes with read-through. I have started by mapping (with STAR) these files with genome to first make a differential expression analysis (with DESeq2). Now I want genes with read-through (with transcription continuing behind TTS). How I can I catch that ?

Maybe a mapper can do it easily ? Or may I have to edit my annotation file to shift end coordinates, and how can I determine a number of nt to shift ? how can I decide if a gene has a read-through by comparing my two mappings ?

Thank you for your help,