How to handle control samples in CLIP-Seq
I've not handled CLIP-seq before, but we have done iCLIP and in this we had controls, but no input. @DevonRyan is correct, these control samples are similar to IgG pulldowns in ChIP seq. 

The way we handled this was to call our peaks on isolated samples. The original peak calling alog from the first CLIP seq paper doesn't require input. Also I believe that clipper doesn't need input (although it will take it). We then removed any peaks from the sample that overlapped a peak in the control. 

But most of our analyses we didn't do on peaks - we did lots of things like looking at metagenes, or classes of genes, or particular types of exon etc, and when we did this, because we were averaging over many sites, we could generate the pattern for the control as well as for the input, and often normalise the one to the other.