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Methods for Annotation and Validation of Circular RNAs from RNAseq Data

  • Disha Sharma
  • Paras Sehgal
  • Judith Hariprakash
  • Sridhar Sivasubbu
  • Vinod ScariaEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1912)

Abstract

Circular RNAs are an emerging class of transcript isoforms created by unique back splicing of exons to form a closed covalent circular structure. While initially considered as product of aberrant splicing, recent evidence suggests unique functions and conservation across evolution. While circular RNAs could be largely attributed to have little or no potential to encode for proteins, recent evidence points to at least a small subset of circular RNAs which encode for peptides. Circular RNAs are also increasingly shown to be biomarkers for a number of diseases including neurological disorders and cancer. The advent of deep sequencing has enabled large-scale identification of circular RNAs in human and other genomes. A number of computational approaches have come up in recent years to query circular RNAs on a genome-wide scale from RNA-seq data. In this chapter, we describe the application and methodology of identifying circular RNAs using three popular computational tools: FindCirc, Segemehl, and CIRI along with approaches for experimental validation of the unique splice junctions.

Key words

Circular RNA circRNAs FindCirc CIRI Segemehl 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Disha Sharma
    • 1
    • 2
  • Paras Sehgal
    • 2
    • 3
  • Judith Hariprakash
    • 1
  • Sridhar Sivasubbu
    • 2
    • 3
  • Vinod Scaria
    • 1
    • 2
    Email author
  1. 1.G.N. Ramachandran Knowledge Center for BioinformaticsCSIR Institute of Genomics and Integrative Biology (CSIR-IGIB)DelhiIndia
  2. 2.Academy of Scientific and Innovative Research (AcSIR)CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB)DelhiIndia
  3. 3.Genomics and Molecular MedicineCSIR Institute of Genomics and Integrative Biology (CSIR-IGIB)DelhiIndia

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