Overlapping PAR-CLIP clusters. (a) Two target sites that would fall into the same cluster by the definition of Hafner et al. , only because in the two DG75 replicates as well as in the second BCBL1 replicate a few random reads from the right target site overlap the left target site. Our cluster definition splits all reads into two overlapping clusters (see the yellow boxes on the bottom). PARma rates both clusters with high Cscores (>0.6 and >0.9 for the left and right clusters, respectively) and assigns the KSHV miRNA kshv-miR-Kl2-7 to the left and the human miRNA hsa-miR-5l9 to the right cluster with MAscores >0.9 in both cases. There is additional evidence that both assignments are correct, since the left cluster has reads only in KSHV positive cell lines (BCBL1, BC1 and BC3) whereas the right cluster contains reads in all experiments. (b) There are hundreds of such cases in both experiments. KSHV: Kaposi's sarcoma-associated herpesvirus.