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Deep Computational Circular RNA Analytics from RNA-seq Data

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1724)

Abstract

Circular RNAs (circRNAs) have been first described as “scrambled exons” in the 1990s. CircRNAs originate from back splicing or exon skipping of linear RNA templates and have continuously gained attention in recent years due to the availability of high-throughput whole-transcriptome sequencing methods. Numerous manuscripts describe thousands of circRNAs throughout uni- and multicellular eukaryote species and demonstrated that they are conserved, stable, and abundant in specific tissues or conditions. This manuscript provides a walk-through of our bioinformatics toolbox, which covers all aspects of in silico circRNA analysis, starting from raw sequencing data and back-splicing junction discovery to circRNA quantitation and reconstruction of internal the circRNA structure.

Key words

Bioinformatics Whole-transcriptome sequencing Circular RNA detection Circular RNA analysis 
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Notes

Acknowledgments

Both authors acknowledge funding by the Klaus Tschira Foundation gGmbH.

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational CardiologyUniversity Hospital HeidelbergHeidelbergGermany
  2. 2.German Center for Cardiovascular Research (DZHK)—Partner site Heidelberg/MannheimHeidelbergGermany

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