Rxivist logo

Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq

By Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter

Posted 09 Sep 2019
bioRxiv DOI: 10.1101/762773

The allocation of a sequencing budget when designing single cell RNA-seq experiments requires consideration of the tradeoff between number of cells sequenced and the read depth per cell. One approach to the problem is to perform a power analysis for a univariate objective such as differential expression. However, many of the goals of single-cell analysis requires consideration of the multivariate structure of gene expression, such as clustering. We introduce an approach to quantifying the impact of sequencing depth and cell number on the estimation of a multivariate generative model for gene expression that is based on error analysis in the framework of a variational autoencoder. We find that at shallow depths, the marginal benefit of deeper sequencing per cell significantly outweighs the benefit of increased cell numbers. Above about 15,000 reads per cell the benefit of increased sequencing depth is minor. Code for the workflow reproducing the results of the paper is available at https://github.com/pachterlab/SBP_2019/.

Download data

  • Downloaded 2,638 times
  • Download rankings, all-time:
    • Site-wide: 2,138 out of 84,950
    • In genomics: 424 out of 5,475
  • Year to date:
    • Site-wide: 3,638 out of 84,950
  • Since beginning of last month:
    • Site-wide: 4,774 out of 84,950

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

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


News