3' end clipping not working

[donutbrew]

Hi there--I have noticed that 3' ends are not clipped. I've played around a little with the -u and -d flags, but nothing seems to really change what is going on with the 3' ends of the reads. Below, I am pasting an IGV plot of what I mean--you can see in the clipped vs unclipped, the primer coverage drops by half--those are only those reads that ahve a primer on the 5' end. Am I missing something? (very possible!) I do need to get both primers clipped, so if I am missing a setting somewhere, please let me know.

[arz19893]

got the same issue, any tips ?

Thanks (: