To be Answered

  • How to accurately compare two CLIP libraries of the same RBP with ~10-fold difference of CLIPped RBP abundance in the cell? How can we account for RBP/target RNA ratio?

  • Is it necessary to use spike ins, and if so, what kind of spike ins and how should I analyse this?

  • How do I choose/remove redundant annotations from genome annotation files?

  • How can I compare multiple RBP baits with different IP efficiencies?

  • What are the best ways to access and analyze published CLIP data?

  • What available pipelines are out there for analysing different CLIP datasets (iCLIP & PAR-CLIP)? Are there advantages/disadvantages to different established pipelines?

  • Which statistical methods are best at identifying cross-link sites?