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bioRxiv · 10.1101/2023.12.21.572723

ChimericFragments: Computation, analysis, and visualization of global RNA networks

Siemers, M.·Lippegaus, A.·Papenfort, K.
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Abstract

RNA-RNA interactions are key for post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA-RNA interactions on a genome-wide scale, computational methods to analyze the underlying data are lagging behind. Here, we present ChimericFragments, an analysis and visualization framework for RNA-seq experiments producing chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and is compatible with several widely used experimental procedures. We demonstrate that ChimericFragments enables the systematic identification of RNA regulators and RNA-RNA pairs and outperforms existing approaches.

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Siemers, M., Lippegaus, A., Papenfort, K.. 2023-12-22. ChimericFragments: Computation, analysis, and visualization of global RNA networks. https://doi.org/10.1101/2023.12.21.572723

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