Comparison of CLIP and iCLIP analysis of Nova binding to its primary RNA target, the Meg3 non-coding RNA. (a) Overview of a region in Meg3 non-coding RNA (chr12: 110800000-110806000). In each panel, the CLIP cDNAs track shows the cluster of CLIP cDNAs without deletions. The CLIP deletions track shows low FDR deletion sites (FDR < 0.001, the positions were re-defined), with peak height corresponding to the number of sequences containing deletions at the sites. The iCLIP truncations track shows the position of iCLIP cDNA truncations (FDR < 0.05), with peak height corresponding to the cDNA counts. The YCAY score track shows the YCAY score at each position, while the YCAYs track shows the position of YCAY motifs. (b) Region with the highest iCLIP cDNA count. This region also has the highest YCAY score. (c) Region with the second highest iCLIP cDNA count. (d) Region with the highest number of CLIP cDNA deletions. Same scale is used in all panels in order to allow comparisons of the evaluated binding sites.