# 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?**<br>