Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome.

ABSTRACT: RNA-seq analysis has enabled the evaluation of transcriptional changes in many species including nonmodel organisms. However, in most species only a single reference genome is available and RNA-seq reads from highly divergent varieties are typically aligned to this reference. Here, we quantify the impacts of the choice of mapping genome in rice where three high-quality reference genomes are available. We aligned RNA-seq data from a popular productive rice variety to three different reference genomes and found that the identification of differentially expressed genes differed depending on which reference genome was used for mapping. Furthermore, the ability to detect differentially used transcript isoforms was profoundly affected by the choice of reference genome: Only 30% of the differenti

SUBMITTER: Slabaugh E 

PROVIDER: S-EPMC6521602 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature