ReviewBMC bioinformatics2021
Comparative evaluation of full-length isoform quantification from RNA-Seq.
Review in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Trustworthy Agentic AI in Bioinformatics: From Workflow Automation to Traceable and Validated Biological Inference.Biology · 2026Review
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- BATF3 regulates differentiation of CD8Life science alliance · 2026Article
- Investigating Alzheimer's Disease-Associated Genes Using Differential Splicing Frequency Analysis.Cells · 2026Article
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
- Improving gene isoform quantification with miniQuant.Nature biotechnology · 2026Article
- RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.GigaScience · 2026Article
- Comparative analysis of ducks liver gene expressions infected with virulent or attenuated DHAV-3 reveals divergent host responses to viruses of different virulence.Frontiers in microbiology · 2026Article
- To be or not to be a protein coding mutation, that's the question!NAR genomics and bioinformatics · 2025Review
- Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain.Genome biology · 2025Article
- Landscape of BRAF transcript variants in human cancer.Molecular oncology · 2025Article
- Long-read RNA sequencing unveils a novel cryptic exon in MNAT1 along with its full-length transcript structure in TDP-43 proteinopathy.Communications biology · 2025Article
- Perplexity as a Metric for Isoform Diversity in the Human Transcriptome.bioRxiv : the preprint server for biology · 2025Article
- Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches.Genome research · 2025Article
- The importance of data transformation in RNA-Seq preprocessing for bladder cancer subtyping.BMC research notes · 2025Article
- Complementary Strategies to Identify Differentially Expressed Genes in the Choroid Plexus of Patients with Progressive Multiple Sclerosis.Neuroinformatics · 2025Article
- Cullin-5 deficiency promotes chimeric antigen receptor T cell effector functions potentially via the modulation of JAK/STAT signaling pathway.Nature communications · 2024Article
- Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python.Bioinformatics (Oxford, England) · 2024Article
- Schizophrenia risk-associated SNPs affect expression of microRNA 137 host gene: a postmortem study.Human molecular genetics · 2024Article
- Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease.American journal of human genetics · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundFull-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short.
resultsHere we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control.
conclusionsSalmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on idealized data, while on more realistic data they do not perform dramatically better than the simple approach. We determine the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms. The effect of incomplete annotation on performance is also investigated. Overall, the tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.