I have 6 aligned BAM files for a species I am working with. We have a single gene we want to see if it's differential. I'd rather not have to run an entire DE analysis when we just want to see if one specific gene is differential. My plan was to extract the gene coordinates and run BedTools coverage to get raw counts. From there, I'd do some type of statistical test (not sure which one) to see if there is a significant difference in the counts.