@article {Vieth583013, author = {Beate Vieth and Swati Parekh and Christoph Ziegenhain and Wolfgang Enard and Ines Hellmann}, title = {A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines: Library preparation and normalisation methods have the biggest impact on the performance of scRNA-seq studies}, elocation-id = {583013}, year = {2019}, doi = {10.1101/583013}, publisher = {Cold Spring Harbor Laboratory}, 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 been established, yet. 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 \~{} 3,000 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, while normalisation dominates pipeline performance in asymmetric DE-setups. Finally, we illustrate the importance of informed choices by showing that a good scRNA-seq pipeline can have the same impact on detecting a biological signal as quadrupling the sample size.}, URL = {https://www.biorxiv.org/content/early/2019/08/05/583013}, eprint = {https://www.biorxiv.org/content/early/2019/08/05/583013.full.pdf}, journal = {bioRxiv} }