A decade ago, the first bioinformatics pipelines to detect circular RNA molecules based on short-read sequencing data were published. Here, we show that dozens of such circular RNA detection tools differ vastly in their sensitivity but not in their specificity.
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References
Salzman, J., Gawad, C., Wang, P. L., Lacayo, N. & Brown, P. O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7, e30733 (2012). This paper reports large-scale circRNA formation from many human genes.
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Vromman, M. et al. Validation of circular RNAs using RT-qPCR after effective removal of linear RNAs by ribonuclease R. Curr. Protoc. 1, e181 (2021). This protocol was used for the validation of more than a thousand circRNAs in the benchmarking study.
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This is a summary of: Vromman, M. et al. Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nat. Methods https://doi.org/10.1038/s41592-023-01944-6 (2023).
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Circular RNA detection pipelines yield divergent sets of circular RNAs. Nat Methods 20, 1135–1136 (2023). https://doi.org/10.1038/s41592-023-01945-5
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DOI: https://doi.org/10.1038/s41592-023-01945-5
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