Fig. 3

Full-length circRNA reconstruction of HeLa cell line (a–c) and human brain (d–f) transcriptomes with RNase R + RiboMinus treatment. a, d CircRNAs reconstructed using both the RO and BSJ features. Completely reconstructed circRNAs are shown in blue-lined ovals. Nearly complete and partial circRNAs are shown in orange and gray, respectively. b, e Length distribution of reconstructed circRNAs in the HeLa cell line and in human whole brain tissue. Complete, nearly complete and partial circRNAs are shown in blue, orange, and gray, respectively. The length of partially reconstructed circRNAs was estimated based on supported BSJ/RO reads and sequencing depth in the RNase R-treated sample. c, f Expression levels of different categories of circRNA. g–j Performance of the RO feature in circRNA identification when applied to fragmented or low-quality RNA samples. The green bar indicates the RNA data set derived from high-quality RNA (RIN = 10) without manual fragmentation. The yellow bar indicates the RNA data set derived from high-quality RNA (RIN = 10) with manual fragmentation. The red bar indicates the RNA data set derived from low-quality RNA (RIN = 5) with manual fragmentation. g, h Comparison of the ratio of RO reads to total circRNA reads for circRNAs of different lengths. ‘**’ and ‘*’ represent P < 0.01 and P < 0.05, respectively (Mann–Whitney U test). i, j Ratio of the number of circular RNAs with RO reads to total circular RNAs of a given length. k Comparison of full-length circRNA structure and corresponding annotated exon regions in human brain tissue. The 150 most highly expressed circRNAs that were completely reconstructed are shown. Each line represents a circRNA with normalized length