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.