Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,077 bioRxiv papers from 306,093 authors.

A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines

By Beate Vieth, Swati Parekh, Christoph Ziegenhain, Wolfgang Enard, Ines Hellmann

Posted 19 Mar 2019
bioRxiv DOI: 10.1101/583013 (published DOI: 10.1038/s41467-019-12266-7)

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.

Download data

  • Downloaded 4,605 times
  • Download rankings, all-time:
    • Site-wide: 534 out of 70,086
    • In bioinformatics: 107 out of 6,878
  • Year to date:
    • Site-wide: 1,109 out of 70,086
  • Since beginning of last month:
    • Site-wide: 3,705 out of 70,086

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)