Question: I have data from my single cell gene expression experiment. Is there software that I can use for removing contamination from ambient RNA in cell-associated barcodes?
Answer: 10x Genomics currently does not have software for removing potential contamination from ambient RNA in individual emulsions. However, you could use the third-party resources listed below. Please note this is an active area of research, the list below may not be comprehensive and you may find more updated information based on your search.
- SoupX
- DecontX
- CellBender (analysis guide: Background Removal Guidance for Single Cell Gene Expression Datasets Using CellBender)
If you have any questions regarding any of the resources above, please contact the respective authors of each article/tool for more information.
If you are just starting to work on your single cell experiment, this TechNote contains information on reducing dead cells and thus ambient mRNA in the sample prep stage.
Disclaimer: This article is provided for instructional purposes only. 10x Genomics does not support or guarantee the listed tools or code.