Hi biostarers, please see the attached picture from RNA-seq of total RNA; that read pairs with the same orientation (RR) that span two adjacent exons. (Supposedly we should see opposite orientation LR for paired-end reads)
I know this indicates inversion for DNA sequencing; but what about in RNA-seq? The same? Or other explanation?
================ Forget that the upper blue bar is simple repeats annotation by repeatmasker. So this intron is highly repetitive, which makes me feel highly suspicious it's circular RNA here given circular RNA formation mediated by flanking repetitive sequence. But the "abnormal" read mapping caused by circular RNA usually mimicks tandem duplication, with two reads still facing opposite but outward.