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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

, , , , and . bioRxiv (2019)

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.

Description

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 | bioRxiv

Links and resources

DOI:
10.1101/583013
URL:
BibTeX key:
Vieth583013
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