I am trying to play with data collection (developped by John Chilton) and I am confused on how to do the Tophat2 step.
I have 5 conditions (triplicates) paired end data. So I have 30 files that I use to create a 'list of dataset pairs'. I end up with that new entity containing 15 pairs. It work fine for grooming, QC and trimming. But when comes the alignment step I select paired end data in tophat2 and then select the collection in both inputs. I end up with a accepted hits for each of the 30 files and not for each pair.
Now I guess I could create 2 list of datasets (1 for forward and 1 for reverse) but it seems weird as the point of collection is to handle pairs. I think I am missing something here but can't figured out what. Can someone clarifies that for me ?