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Normalizing single-cell RNA sequencing data: challenges and opportunities.

ABSTRACT: Single-cell transcriptomics is becoming an important component of the molecular biologist's toolkit. A critical step when analyzing data generated using this technology is normalization. However, normalization is typically performed using methods developed for bulk RNA sequencing or even microarray data, and the suitability of these methods for single-cell transcriptomics has not been assessed. We here discuss commonly used normalization approaches and illustrate how these can produce misleading results. Finally, we present alternative approaches and provide recommendations for single-cell RNA sequencing users.

SUBMITTER: Vallejos CA

PROVIDER: S-EPMC5549838 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Normalizing single-cell RNA sequencing data: challenges and opportunities.

Vallejos Catalina A CA Risso Davide D Scialdone Antonio A Dudoit Sandrine S Marioni John C JC

Nature methods 20170515 6

Single-cell transcriptomics is becoming an important component of the molecular biologist's toolkit. A critical step when analyzing data generated using this technology is normalization. However, normalization is typically performed using methods developed for bulk RNA sequencing or even microarray data, and the suitability of these methods for single-cell transcriptomics has not been assessed. We here discuss commonly used normalization approaches and illustrate how these can produce misleading ...[more]

PMID: 28504683

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