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- Title
RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.
- Authors
Singh, Sandeep; Shi, Xinrui; Haddox, Samuel; Elfman, Justin; Ahmad, Syed Basil; Lynch, Sarah; Manley, Tommy; Piczak, Claire; Phung, Christopher; Sun, Yunan; Sharma, Aadi; Li, Hui
- Abstract
Read-through chimeric RNAs are being recognized as a means to expand the functional transcriptome and contribute to cancer tumorigenesis when mis-regulated. However, current software tools often fail to predict them. We have developed RTCpredictor, utilizing a fast ripgrep tool to search for all possible exon-exon combinations of parental gene pairs. We also added exonic variants allowing searches containing common SNPs. To our knowledge, it is the first read-through chimeric RNA specific prediction method that also provides breakpoint coordinates. Compared with 10 other popular tools, RTCpredictor achieved high sensitivity on a simulated and three real datasets. In addition, RTCpredictor has less memory requirements and faster execution time, making it ideal for applying on large datasets.
- Subjects
RNA sequencing; RNA; SOFTWARE development tools; TRANSCRIPTOMES; SINGLE nucleotide polymorphisms
- Publication
Briefings in Bioinformatics, 2024, Vol 25, Issue 4, p1
- ISSN
1467-5463
- Publication type
Article
- DOI
10.1093/bib/bbae251