Detecting circular RNA from high-throughput sequence data with de Bruijn graph

BMC Genomics
Xin Li, Yufeng Wu

Abstract

Circular RNA is a type of non-coding RNA, which has a circular structure. Many circular RNAs are stable and contain exons, but are not translated into proteins. Circular RNA has important functions in gene regulation and plays an important role in some human diseases. Several biological methods, such as RNase R treatment, have been developed to identify circular RNA. Multiple bioinformatics tools have also been developed for circular RNA detection with high-throughput sequence data. In this paper, we present circDBG, a new method for circular RNA detection with de Bruijn graph. We conduct various experiments to evaluate the performance of CircDBG based on both simulated and real data. Our results show that CircDBG finds more reliable circRNA with low bias, has more efficiency in running time, and performs better in balancing accuracy and sensitivity than existing methods. As a byproduct, we also introduce a new method to classify circular RNAs based on reads alignment. Finally, we report a potential chimeric circular RNA that is found by CircDBG based on real sequence data. CircDBG can be downloaded from https://github.com/lxwgcool/CircDBG. We develop a new method called CircDBG for circular RNA detection, which is based on de ...Continue Reading

References

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Citations

Feb 7, 2020·BMC Evolutionary Biology·Iker IrisarriRafael Zardoya
Sep 11, 2020·BioMed Research International·Min TangWenqiang Chen

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Datasets Mentioned

BETA
SRR4095542
SRR5133906

Methods Mentioned

BETA
RNA-seq

Software Mentioned

CIRI
circRNA
CircRNAFinder
CircDBG
CIRI2
BWA
CircMarker
Find
Bowtie
circ

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