Deep Computational Circular RNA Analytics from RNA-seq Data
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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 wordsBioinformatics Whole-transcriptome sequencing Circular RNA detection Circular RNA analysis
Both authors acknowledge funding by the Klaus Tschira Foundation gGmbH.
- 5.Dodt M, Roehr JT, Ahmed R, Dieterich C (2012) FLEXBAR—flexible barcode and adapter processing for next-generation sequencing platforms. Biology (Basel) 1(3):895–905Google Scholar
- 17.R Core Team (2013) R: a language and environment for statistical computing. Vienna, AustriaGoogle Scholar
- 18.Andrews S (2012) FastQC. A Qual. Control tool high throughput Seq. data. [http//www.bioinformatics.bbsrc.ac.uk/projects/fastqc/]Google Scholar