A systematic evaluation of single cell RNA-seq analysis pipelines.

ABSTRACT: The recent rapid spread of single cell RNA sequencing (scRNA-seq) methods has created a large variety of experimental and computational pipelines for which best practices have not yet been established. Here, we use simulations based on five scRNA-seq library protocols in combination with nine realistic differential expression (DE) setups to systematically evaluate three mapping, four imputation, seven normalisation and four differential expression testing approaches resulting in ~3000 pipelines, allowing us to also assess interactions among pipeline steps. We find that choices of normalisation and library preparation protocols have the biggest impact on scRNA-seq analyses. Specifically, we find that library preparation determines the ability to detect symmetric expression differences, whil

SUBMITTER: Vieth B 

PROVIDER: S-EPMC6789098 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature