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bioRxiv · 10.1101/2023.02.02.526869

RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data

Singh, S.·Shi, X.·Ahmad, S.·Manley, T.·Piczak, C.·Phung, C.·Sun, Y.·Lynch, S.·Sharma, A.·Li, H.
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Abstract

Read-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor (https://github.com/sandybioteck/RTCpredictor) has less memory requirements and faster execution time.

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Singh, S., Shi, X., Ahmad, S., Manley, T., Piczak, C., Phung, C., Sun, Y., Lynch, S., Sharma, A., Li, H.. 2023-02-03. RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data. https://doi.org/10.1101/2023.02.02.526869

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