ArticleCell systems2019
Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Bramble: projection of spliced genomic alignments into transcriptomic space for improved transcript quantification.bioRxiv : the preprint server for biology · 2026Article
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- Singletrome enhances detection of long noncoding RNAs in single cell transcriptomes.Scientific reports · 2025Article
- De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide.Frontiers in zoology · 2024Review
- BELMM: Bayesian model selection and random walk smoothing in time-series clustering.Bioinformatics (Oxford, England) · 2023Article
- Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients.Frontiers in oncology · 2022Review
- Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments.Genome research · 2021Article
- Effect of de novo transcriptome assembly on transcript quantification.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Because of incomplete reference transcriptomes, incomplete sequencing bias models, or other modeling defects, algorithms to infer isoform expression from RNA sequencing (RNA-seq) sometimes do not accurately model expression. We present a computational method to detect instances where a quantification algorithm could not completely explain the input reads. Our approach identifies regions where the read coverage significantly deviates from expectation. We call these regions "expression anomalies." We further present a method to attribute their cause to either the incompleteness of the reference transcriptome or algorithmic mistakes. We detect anomalies for 30 GEUVADIS and 16 Human Body Map samples. By correcting anomalies when possible, we reduce the number of falsely predicted instances of differential expression. Anomalies that cannot be corrected are suspected to indicate the existence of isoforms unannotated by the reference. We detected 88 common anomalies of this type and find that they tend to have a lower-than-expected coverage toward their 3' ends.
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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.