Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope

Neetha Nanoth Vellichirammal, Abrar Albahrani, You Li, Chittibabu Guda

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Fusion transcripts that are frequent in cancer can be exploited to understand the mechanisms of malignancy and can serve as diagnostic or prognostic markers. Several algorithms have been developed to predict fusion transcripts from DNA or RNA data. The majority of these algorithms align sequencing reads to the reference transcriptome for predicting fusions; however, this results in several undetected fusions due to the highly perturbed nature of cancer genomes. Here, we describe a novel method that uses a k-mer based algorithm to predict fusion transcripts accurately using the unaligned reads from the regular RNA-seq data analysis pipelines.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages13-25
Number of pages13
DOIs
StatePublished - 2020

Publication series

NameMethods in Molecular Biology
Volume2079
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • ChimeRScope
  • Fusion detection algorithm
  • Fusion transcripts
  • Oncogenic fusions
  • RNA-seq
  • k-mers

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Vellichirammal, N. N., Albahrani, A., Li, Y., & Guda, C. (2020). Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope. In Methods in Molecular Biology (pp. 13-25). (Methods in Molecular Biology; Vol. 2079). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9904-0_2