ArticleScientific reports2016
Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed.
- PFGPred: a stack ensemble classifier for the identification of fusion genes in plants.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
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- Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies.NPJ precision oncology · 2026Article
- GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data.Briefings in bioinformatics · 2026Article
- Whole transcriptome analysis identifiesCancer pathogenesis and therapy · 2025Article
- Article
- SplitFusion enables ultrasensitive gene fusion detection and reveals fusion variant-associated tumor heterogeneity.Patterns (New York, N.Y.) · 2025Article
- Molecular and expression analyses indicate the role of fusion transcripts in mediating abiotic stress responses in chickpea.Frontiers in plant science · 2025Article
- Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.Methods in molecular biology (Clifton, N.J.) · 2025Article
- OncogenicMedComm · 2024Article
- Precision Medicine in Cytopathology.Surgical pathology clinics · 2024Review
- RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.Briefings in bioinformatics · 2024Article
- A Protocol for the Detection of Fusion Transcripts Using RNA-Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- TargetedCell reports methods · 2023Article
- Recent advances in cancer fusion transcript detection.Briefings in bioinformatics · 2023Review
- Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods.Computational and structural biotechnology journal · 2023Review
- Fusion InPipe, an integrative pipeline for gene fusion detection from RNA-seq data in acute pediatric leukemia.Frontiers in molecular biosciences · 2023Article
- mRNA Capture Sequencing and RT-qPCR for the Detection of Pathognomonic, Novel, and Secondary Fusion Transcripts in FFPE Tissue: A Sarcoma Showcase.International journal of molecular sciences · 2022Article
- Regulatory networks and 5' partner usage of miRNA host gene fusions in breast cancer.International journal of cancer · 2022Article
- Standardized evidence-based approach for assessment of oncogenic and clinical significance of NTRK fusions.Cancer genetics · 2022Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
RNA-Seq made possible the global identification of fusion transcripts, i.e. "chimeric RNAs". Even though various software packages have been developed to serve this purpose, they behave differently in different datasets provided by different developers. It is important for both users, and developers to have an unbiased assessment of the performance of existing fusion detection tools. Toward this goal, we compared the performance of 12 well-known fusion detection software packages. We evaluated the sensitivity, false discovery rate, computing time, and memory usage of these tools in four different datasets (positive, negative, mixed, and test). We conclude that some tools are better than others in terms of sensitivity, positive prediction value, time consumption and memory usage. We also observed small overlaps of the fusions detected by different tools in the real dataset (test dataset). This could be due to false discoveries by various tools, but could also be due to the reason that none of the tools are inclusive. We have found that the performance of the tools depends on the quality, read length, and number of reads of the RNA-Seq data. We recommend that users choose the proper tools for their purpose based on the properties of their RNA-Seq data.
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