ArticleBMC genomics2017
Evaluation and comparison of computational tools for RNA-seq isoform quantification.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
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Who cites it
102 citing papers in PubMed.
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- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
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- SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis.Computational and structural biotechnology journal · 2026Article
- Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain.Genome biology · 2025Article
- Perplexity as a Metric for Isoform Diversity in the Human Transcriptome.bioRxiv : the preprint server for biology · 2025Article
- Identification of potential biomarkers for hypertension based on transcriptomic analysis in rats.Hypertension research : official journal of the Japanese Society of Hypertension · 2025Article
- A microfluidic bone marrow chip for the safety profiling of biologics in pre-clinical drug development.Communications biology · 2025Article
- A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.Nature methods · 2025Article
- Transcriptomic Analysis ofPlants (Basel, Switzerland) · 2025Article
- The importance of data transformation in RNA-Seq preprocessing for bladder cancer subtyping.BMC research notes · 2025Article
- Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python.Bioinformatics (Oxford, England) · 2024Article
- Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofGenome research · 2024Article
- CD9 shapes glucocorticoid sensitivity in pediatric B-cell precursor acute lymphoblastic leukemia.Haematologica · 2024Article
- Reference-free inferring of transcriptomic events in cancer cells on single-cell data.BMC cancer · 2024Article
- Probing Liver Injuries Induced by Thioacetamide in Human In Vitro Pooled Hepatocyte Experiments.International journal of molecular sciences · 2024Article
- Accounting for isoform expression increases power to identify genetic regulation of gene expression.PLoS computational biology · 2024Article
42 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
backgroundAlternatively spliced transcript isoforms are commonly observed in higher eukaryotes. The expression levels of these isoforms are key for understanding normal functions in healthy tissues and the progression of disease states. However, accurate quantification of expression at the transcript level is limited with current RNA-seq technologies because of, for example, limited read length and the cost of deep sequencing.
resultsA large number of tools have been developed to tackle this problem, and we performed a comprehensive evaluation of these tools using both experimental and simulated RNA-seq datasets. We found that recently developed alignment-free tools are both fast and accurate. The accuracy of all methods was mainly influenced by the complexity of gene structures and caution must be taken when interpreting quantification results for short transcripts. Using TP53 gene simulation, we discovered that both sequencing depth and the relative abundance of different isoforms affect quantification accuracy
conclusionsOur comprehensive evaluation helps data analysts to make informed choice when selecting computational tools for isoform quantification.
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