Highly accurate quantification of allelic gene expression for population and disease genetics.

ABSTRACT: Analysis of allele-specific gene expression (ASE) is a powerful approach for studying gene regulation, particularly when sample sizes are small, such as for rare diseases, or when studying the effects of rare genetic variation. However, detection of ASE events relies on accurate alignment of RNA sequencing reads, where challenges still remain, particularly for reads containing genetic variants or those that align to many different genomic locations. We have developed the Personalised ASE Caller (PAC), a tool that combines multiple steps to improve the quantification of allelic reads, including personalized (i.e., diploid) read alignment with improved allocation of multimapping reads. Using simulated RNA sequencing data, we show that PAC outperforms standard alignment a

SUBMITTER: Saukkonen A 

PROVIDER: S-EPMC9435737 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature