ArticleNature methods2013
Systematic evaluation of spliced alignment programs for RNA-seq data.
Article in Nature methods, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 307 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
307 citing papers in PubMed.
- A Randomized Phase II Neoadjuvant Study of Cisplatin, Paclitaxel With or Without Everolimus in Patients with Stage II/III Triple-Negative Breast Cancer (TNBC): Responses and Long-term Outcome Correlated with Increased Frequency of DNA Damage Response Gene Mutations, TNBC Subtype, AR Status, and Ki67.Clinical cancer research : an official journal of the American Association for Cancer Research · 2017Trial
- Aberrant splicing in human cancer shows possible functional impact on transcription factors.Oncogene · 2026Article
- AXIN1 and AXIN2 regulate the WNT-signaling landscape to promote distinct mesoderm programs.Developmental cell · 2026Article
- Recent advances in the detection and functional analysis of circRNAs with short-read RNA sequencing-based methods.Molecular biology reports · 2026Review
- At the Edge of Survival: Exploring the Frontiers of Tardigrade Extreme Stress Tolerance.Molecular ecology · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Chronic ethanol drinking alters medial prefrontal cortex and nucleus accumbens astrocyte translatome and extracellular matrix glycosaminoglycans.Neuropharmacology · 2026Article
- Efficient reconstruction of full-length RNA isoforms using ISAtools and large-scale PacBio circular consensus sequencing data.Briefings in bioinformatics · 2026Article
- Chronic alcohol consumption sex-dependently affects IL-6 modulation of GABAergic synapses in the central amygdala of rhesus macaques.Brain, behavior, and immunity · 2026Article
- A Global Assessment of the Transcription-Dependent Single Nucleotide Variants Relies on the Characteristics of RNA-Sequencing Technologies.Biomolecules · 2026Article
- Intestinal epithelial TLR5 signaling promotes barrier-supportive macrophages.Science immunology · 2026Article
- Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter.Nucleic acids research · 2026Article
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- AI/ML-Driven Gene Analysis: New Perspectives on Variant Calling in Normal Human Tissue Using scRNA-seq Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Chronic Ethanol Drinking Alters Medial Prefrontal Cortex and Nucleus Accumbens Astrocyte Translatome and Extracellular Matrix Glycosaminoglycans.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive Transcriptome Annotation of Thousands of HIV-1 Genomes.bioRxiv : the preprint server for biology · 2025Article
- SARS-CoV-2 Nsp2 recruits GIGYF2 near viral replication sites and supports viral protein production.Nucleic acids research · 2025Article
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Analysis of allohexaploid wheatgrass genome reveals its Y haplome origin in Triticeae and high-altitude adaptation.Nature communications · 2025Article
- Detection of mRNA Transcript Variants.Genes · 2025Review
247 more citing papers are in PubMed but not listed here.
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12 authors.
Funding
Abstract
High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions.
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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.