When displaying individual reads in the AlignmentTrack, I can see the orientation of each read by an arrow shape, but only if I am zoomed in enough.  Once I'm zoomed out a bit, I lose that information (each read is simply a rectangle). Is there a way I can control this behavior?  Or perhaps color reads based on their orientation?  Ideally, I'd like to highlight read pairs that have different orientations (FF, FR, RR, etc.).  Thanks for any suggestions.

Hi Lance,

currently there is no control over the exact colouring of the reads, but your use case makes perfect sense and it shouldn't be too hard to implement. I will take a look and make sure to add this to the next release.

Florian