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. 2023 Jul 20;24:171. doi: 10.1186/s13059-023-03012-w

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — Long-read RNA-seq detected highly structured regions. a IGV plot for an example where many reads had internal skipping. This region harbors two Alus. The double-strand RNA structure predicted by RNAfold is shown. b Diagram illustrating RT-induced template switching that may induce region-skipping in long reads. c Read coverage of predicted dsRNAs with or without region-skipping patterns. d Histogram of dsRNAs with different fractions of reads that showed region-skipping patterns. e The length of skipped regions within predicted dsRNAs (median = 813, 627 for the AD and GM12878 data, respectively)