ArticleBioinformatics (Oxford, England)2015
Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- MASQ: A multiplex qPCR platform for quantitative alternative splicing analysis in clinical specimens.Molecular therapy. Nucleic acids · 2026Article
- Investigating Alzheimer's Disease-Associated Genes Using Differential Splicing Frequency Analysis.Cells · 2026Article
- A deep dive into statistical modeling of RNA splicing QTLs reveals variants that explain neurodegenerative disease.American journal of human genetics · 2025Article
- High Overexpression ofInternational journal of molecular sciences · 2024Article
- Challenges and best practices in omics benchmarking.Nature reviews. Genetics · 2024Review
- ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs.BMC bioinformatics · 2024Article
- Transcriptomic signatures across a critical sedimentation threshold in a major reef-building coral.Frontiers in physiology · 2024Article
- Alternative splicing analysis benchmark with DICAST.NAR genomics and bioinformatics · 2023Article
- A study of differential microRNA expression profile in migraine: the microMIG exploratory study.The journal of headache and pain · 2023Article
- The hitchhikers' guide to RNA sequencing and functional analysis.Briefings in bioinformatics · 2023Article
- The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma.NAR cancer · 2022Article
- Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing.Methods in molecular biology (Clifton, N.J.) · 2022Article
- CAMPAREE: a robust and configurable RNA expression simulator.BMC genomics · 2021Article
- McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data.Bioinformatics (Oxford, England) · 2021Article
- Article
- Modular, efficient and constant-memory single-cell RNA-seq preprocessing.Nature biotechnology · 2021Article
- LIQA: long-read isoform quantification and analysis.Genome biology · 2021Article
- Comparative evaluation of full-length isoform quantification from RNA-Seq.BMC bioinformatics · 2021Review
- LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.BMC genomics · 2020Article
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Authors and funding
5 authors.
Funding
Abstract
motivationBecause of the advantages of RNA sequencing (RNA-Seq) over microarrays, it is gaining widespread popularity for highly parallel gene expression analysis. For example, RNA-Seq is expected to be able to provide accurate identification and quantification of full-length splice forms. A number of informatics packages have been developed for this purpose, but short reads make it a difficult problem in principle. Sequencing error and polymorphisms add further complications. It has become necessary to perform studies to determine which algorithms perform best and which if any algorithms perform adequately. However, there is a dearth of independent and unbiased benchmarking studies. Here we take an approach using both simulated and experimental benchmark data to evaluate their accuracy.
resultsWe conclude that most methods are inaccurate even using idealized data, and that no method is highly accurate once multiple splice forms, polymorphisms, intron signal, sequencing errors, alignment errors, annotation errors and other complicating factors are present. These results point to the pressing need for further algorithm development. AVAILABILITY AND IMPLEMENTATION: Simulated datasets and other supporting information can be found at http://bioinf.itmat.upenn.edu/BEERS/bp2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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