Fig. 1

Mispriming on genomic occurrences of the 3′ adaptor sequence produces an artifact in HITS-CLIP data. a Occurrences of the first six bases of the 3′ adaptor (allowing for one mismatch) in 200 bp windows around peak centers plotted using 20 bp sliding windows (with a 6 bp shift between each window) relative to the expected frequency of each adaptor-complement (calculated using 1 x 10⁶ randomly sampled exonic sequences of 200 bp). Our early samples (emerald; 6 samples from 1 research group) show consistent overrepresentation of the adaptor sequence. This overrepresentation is also seen in a group of published samples (blue; 25 samples from 10 groups), while another group of published samples show underrepresentation of the adaptor sequence at the center of the peak (vermilion; 19 samples from 9 groups). The samples with the most extreme over- and underrepresentation are shown as dashed blue and vermilion lines, respectively. b Percentage of peaks containing the first six bases of the 3′ adaptor sequence (allowing for one mismatch) between positions −25 and +75 in each peak (highlighted in grey in A), minus the expected frequency (calculated using 1 x 10⁶ randomly sampled exonic sequences of 200 bp). Groups are the same as in (a)