I want to detect circular RNAs with paired-end RNA-seq data. My assumption is, that during the alignment to the Genome (STAR 2.7.0f) I would expect STAR to encounter issues regarding the directionality of the paired-end reads since the expected second mate of the read can be upstream instead of downstream in a circular alignment.

Does Star still include such reads and is there a way to mark these and flag/extract them to analyze cases in which this happens potentially also for circular RNA detection?

I am aware of the --chimSegmentMin option in STAR to allow circular or chimeric reads, yet this option seems to be just for the read itself, yet I am also interested in how to detect pair in which the insert of the paired-end read would lead to a chimeric form since of circularization.

I would be glad for the help and try to better explain my problem if people having issues understanding it.

Greetings & Thanks! David