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RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.
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.
Affiliation
  • Singh S; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Shi X; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Haddox S; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Elfman J; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Ahmad SB; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Lynch S; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Manley T; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Piczak C; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Phung C; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Sun Y; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Sharma A; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
  • Li H; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States.
Brief Bioinform ; 25(4)2024 May 23.
Article in En | MEDLINE | ID: mdl-38796690
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Sequence Analysis, RNA Limits: Humans Language: En Journal: Brief Bioinform / Brief. bioinform / Briefings in bioinformatics Journal subject: BIOLOGIA / INFORMATICA MEDICA Year: 2024 Document type: Article Affiliation country: Estados Unidos Country of publication: Reino Unido
Fulltext
Add to My VHL
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Sequence Analysis, RNA Limits: Humans Language: En Journal: Brief Bioinform / Brief. bioinform / Briefings in bioinformatics Journal subject: BIOLOGIA / INFORMATICA MEDICA Year: 2024 Document type: Article Affiliation country: Estados Unidos Country of publication: Reino Unido