RT Journal Article
SR Electronic
T1 A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
JF Life Science Alliance
JO Life Sci. Alliance
FD Life Science Alliance LLC
SP e201800175
DO 10.26508/lsa.201800175
VO 2
IS 1
A1 Charlotte Soneson
A1 Michael I Love
A1 Rob Patro
A1 Shobbir Hussain
A1 Dheeraj Malhotra
A1 Mark D Robinson
YR 2019
UL https://www.life-science-alliance.org/content/2/1/e201800175.abstract
AB 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.