Hihi, I have maybe a bit of a side question ... I was asked what type of control I would recommend apart from the typical eCLIP SM Input control for a iCLIP experiment. So far we are always using CLIP data without controls and instead have peakcallers that do not need controls ... however, sometimes I feel from a computational point of view, having a control could make life much easier ... I have the feeling that different PIs have very strong opinions on this ^^ but how are you handling this? Any recommendations for a good control? Or would you also say it is better to continue computational analyses without controls?

In my experience, total RNAseq is much better control than SM input - more coverage and more uniform. OmniCLIP and I think PureCLIP too can take it as background.

Ok interesting. I will ask them if they would try 🙂 . Would you still do Ribodepletion on the total RNAseq? Probably yes?

Yes, mostly this is standard.