Title | A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. |
Publication Type | Journal Article |
Year of Publication | 2019 |
Authors | Soneson, Charlotte, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, and Mark D. Robinson |
Journal | Life Sci Alliance |
Volume | 2 |
Issue | 1 |
Date Published | 2019 Feb |
ISSN | 2575-1077 |
Keywords | 3' Untranslated Regions, Data Accuracy, Exons, Genes, Genome, Human, Genomic Library, Humans, Introns, Protein Isoforms, Reproducibility of Results, Research Design, RNA Precursors, RNA-Seq, Transcriptome |
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. |
DOI | 10.26508/lsa.201800175 |
Alternate Journal | Life Sci Alliance |
Original Publication | A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. |
PubMed ID | 30655364 |
PubMed Central ID | PMC6337739 |
Grant List | P30 ES010126 / ES / NIEHS NIH HHS / United States BB/N000749/1 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom P01 CA142538 / CA / NCI NIH HHS / United States R01 HG009937 / HG / NHGRI NIH HHS / United States R01 HG009125 / HG / NHGRI NIH HHS / United States |
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.
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