Hello,

Quick question: I have a dUTP RNAseq library prep. I would like to infer antisense ncRNAs with Rockhopper. Specifying read orientation as F/R or R/F logically yields different results... However, researching the differential use of F/R and R/F between the various programs has left me confused as to which program setting is appropriate for dUTP prep in Rockhopper. Any help out there?

Any help would be greatly appreciated.

Thanks!