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RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.
- Source :
-
Briefings in bioinformatics [Brief Bioinform] 2024 May 23; Vol. 25 (4). - Publication Year :
- 2024
-
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.<br /> (© The Author(s) 2024. Published by Oxford University Press.)
Details
- Language :
- English
- ISSN :
- 1477-4054
- Volume :
- 25
- Issue :
- 4
- Database :
- MEDLINE
- Journal :
- Briefings in bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 38796690
- Full Text :
- https://doi.org/10.1093/bib/bbae251