A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.

TitleA junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.
Publication TypeJournal Article
Year of Publication2019
AuthorsSoneson, Charlotte, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, and Mark D. Robinson
JournalLife Sci Alliance
Volume2
Issue1
Date Published2019 02
ISSN2575-1077
Keywords3' 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.

DOI10.26508/lsa.201800175
Alternate JournalLife Sci Alliance
Original PublicationA junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.
PubMed ID30655364
PubMed Central IDPMC6337739
Grant ListP30 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
Project: