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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.

2023-02-03 genomics
10.1101/2023.02.02.526869 bioRxiv
Show 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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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.