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Related Experiment Video

Updated: Mar 10, 2026

Identification of Circular RNAs using RNA Sequencing
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Identification of Circular RNAs using RNA Sequencing

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Acfs: accurate circRNA identification and quantification from RNA-Seq data.

Xintian You1, Tim Of Conrad1,2

  • 1Department of Numerical Mathematics, The Zuse Institute Berlin, Berlin, 14195, Germany.

Scientific Reports
|December 9, 2016
PubMed
Summary

A new software tool, acfs, accurately identifies circular RNAs (circRNAs) from RNA sequencing data. This advancement aids in understanding circRNA roles in diseases like leukemia and enables fusion circRNA detection.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Circular RNAs (circRNAs) are prevalent, functionally significant RNA molecules.
  • Their characterization is crucial for understanding development and disease.
  • Existing tools may lack accuracy or efficiency in circRNA identification.

Purpose of the Study:

  • To introduce acfs, a novel software package for circRNA identification and quantification.
  • To evaluate acfs performance against existing state-of-the-art tools.
  • To demonstrate the utility of circRNA profiling in disease contexts, such as leukemia.

Main Methods:

  • Development of the acfs software package for de novo circRNA detection.
  • Performance evaluation using simulated and real-world RNA-Seq datasets.
  • Application of acfs to analyze circRNA expression in leukemia patient samples.

Main Results:

  • Acfs achieved superior accuracy (highest F1 score) and a lower false discovery rate (FDR) compared to other tools on simulated data.
  • Acfs identified more bona fide circRNAs efficiently from real-world datasets.
  • Differential circRNA expression was observed between AML and APL samples, and fusion circRNAs were detected.

Conclusions:

  • Acfs provides an accurate, fast, and efficient method for genome-wide circRNA characterization.
  • CircRNA profiling holds potential for molecular classification of complex diseases.
  • Acfs is a versatile tool for diverse applications, including cancer biology and non-model organisms.