Abstract
RNA structure is a key player in regulating a plethora of biological processes. A large part of the functions carried out by RNA is mediated by its structure. To this end, in the last decade big effort has been put in the development of new RNA probing methods based on Next-Generation Sequencing (NGS), aimed at the rapid transcriptome-scale interrogation of RNA structures. In this chapter we describe RNA Framework, the to date most comprehensive toolkit for the analysis of NGS-based RNA structure probing experiments. By using two published datasets, we here illustrate how to use the different components of the RNA Framework and how to choose the analysis parameters according to the experimental setup.
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Acknowledgments
This work was supported by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO; OCENW.XS3.044) and by funding of the University of Groningen (Groningen, the Netherlands) and the Groningen Biomolecular Sciences and Biotechnology Institute (GBB) to D.I.
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Marinus, T., Incarnato, D. (2021). RNA Framework for Assaying the Structure of RNAs by High-Throughput Sequencing. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 2284. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1307-8_5
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DOI: https://doi.org/10.1007/978-1-0716-1307-8_5
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