Question: How can I aggregate or compare single-cell libraries between species?
Answer: Cell Ranger does not support aggregating libraries from different reference genomes. However, here are some third party tools that you might find useful.
- Davie et al. 2018. A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain. https://doi.org/10.1016/j.cell.2018.05.057
- There is a note about a tool called SCope that can do between-species comparisons.
- Butler et al. 2018. Integrating single-cell transcriptomic data across different conditions, technologies, and species. https://www.nature.com/articles/nbt.4096
Unfortunately we are not staffed to provide support for third party tools. Questions regarding these should be directed to the corresponding authors of these papers. Please note that this is not an exhaustive list and there may be other available tools that are not listed.