ArticleLife science alliance2019
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.
Article in Life science alliance, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.Genome biology · 2026Article
- Detection of alternative splicing: deep sequencing or deep learning?Briefings in bioinformatics · 2026Article
- Improved characterization of 3' single-cell RNA-seq libraries with paired-end avidity sequencing.NAR genomics and bioinformatics · 2024Article
- Improved characterization of single-cell RNA-seq libraries with paired-end avidity sequencing.bioRxiv : the preprint server for biology · 2024Article
- Targeting CCR7-PI3Kγ overcomes resistance to tyrosine kinase inhibitors in ALK-rearranged lymphoma.Science translational medicine · 2023Article
- Hyaluronan nanoscale clustering and Hyaluronan synthase 2 expression are linked to the invasion of child fibroblasts and infantile fibrosarcoma in vitro and in vivo.Scientific reports · 2022Article
- High-quality reference transcriptome construction improves RNA-seq quantification inFrontiers in genetics · 2022Article
- Chromatin loop anchors predict transcript and exon usage.Briefings in bioinformatics · 2021Article
- 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists.RNA biology · 2021Article
- Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification.Cell systems · 2019Article
- BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.BMC genomics · 2019Article
- Effect of de novo transcriptome assembly on transcript quantification.Scientific reports · 2019Article
- Genetic effects on promoter usage are highly context-specific and contribute to complex traits.eLife · 2019Article
- Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase (F1000Research · 2018Article
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6 authors.
Funding
Abstract
Most methods for statistical analysis of RNA-seq data take a matrix of abundance estimates for some type of genomic features as their input, and consequently the quality of any obtained results is directly dependent on the quality of these abundances. Here, we present the junction coverage compatibility score, which provides a way to evaluate the reliability of transcript-level abundance estimates and the accuracy of transcript annotation catalogs. It works by comparing the observed number of reads spanning each annotated splice junction in a genomic region to the predicted number of junction-spanning reads, inferred from the estimated transcript abundances and the genomic coordinates of the corresponding annotated transcripts. We show that although most genes show good agreement between the observed and predicted junction coverages, there is a small set of genes that do not. Genes with poor agreement are found regardless of the method used to estimate transcript abundances, and the corresponding transcript abundances should be treated with care in any downstream analyses.
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