ArticleNucleic acids research2018
The fractured landscape of RNA-seq alignment: the default in our STARs.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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.
The trial behind it
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
11 citing papers in PubMed.
- Histone methyltransferase Setd8 preserves chromatin accessibility to safeguard retinal progenitor cell identity during development.Stem cell reports · 2026Article
- Wnt3a/GSK3β/β-catenin Signalling Modulates Doxorubicin-associated Memory Deficits in Breast Cancer.Molecular neurobiology · 2024Article
- BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens.Genome biology · 2023Article
- Sexing of cattle embryos using RNA-sequencing data or polymerase chain reaction based on a complete sequence of cattle chromosome Y.Frontiers in genetics · 2023Article
- Histone chaperone HIRA complex regulates retrotransposons in embryonic stem cells.Stem cell research & therapy · 2022Article
- SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.BMC bioinformatics · 2021Article
- Systematic evaluation of differential splicing tools for RNA-seq studies.Briefings in bioinformatics · 2020Article
- Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures.NAR genomics and bioinformatics · 2020Article
- Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome.Cell reports · 2019Article
- Article
- The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function.Nucleic acids research · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Many tools are available for RNA-seq alignment and expression quantification, with comparative value being hard to establish. Benchmarking assessments often highlight methods' good performance, but are focused on either model data or fail to explain variation in performance. This leaves us to ask, what is the most meaningful way to assess different alignment choices? And importantly, where is there room for progress? In this work, we explore the answers to these two questions by performing an exhaustive assessment of the STAR aligner. We assess STAR's performance across a range of alignment parameters using common metrics, and then on biologically focused tasks. We find technical metrics such as fraction mapping or expression profile correlation to be uninformative, capturing properties unlikely to have any role in biological discovery. Surprisingly, we find that changes in alignment parameters within a wide range have little impact on both technical and biological performance. Yet, when performance finally does break, it happens in difficult regions, such as X-Y paralogs and MHC genes. We believe improved reporting by developers will help establish where results are likely to be robust or fragile, providing a better baseline to establish where methodological progress can still occur.
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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.