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?