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RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.

Authors :
Singh S
Shi X
Haddox S
Elfman J
Ahmad SB
Lynch S
Manley T
Piczak C
Phung C
Sun Y
Sharma A
Li H
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