Question: How can we impute dropouts in our scRNAseq data?
Answer: We don't have any direct experience with dropout imputation. However there is a growing literature on this topic. Please see:
- Wei Vivian Li & Jingyi Jessica Li. An accurate and robust imputation method scImpute for single-cell RNA-seq data. Nature Communications, 9, 997. https://doi.org/10.1038/s41467-018-03405-7 (2018)
- Huang, M. et al. Gene expression recovery for single cell RNA sequencing. bioRxiv Preprint available from https://doi.org/10.1101/138677 (2017).
- van Dijk, D. et al. Magic: a diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data. bioRxiv Preprint available from https://doi.org/10.1101/111591 (2017).
Please note that we do not have much experience with imputation and we would recommend extreme precaution in case you choose to proceed with using any imputation methods. Any of the methods listed above are not officially supported, tested or endorsed by 10x Genomics.