Question: Why do I find nuclei aggregates in a barcode rank plot and how to use my data
Answer: For some complex nuclei samples, the Barcode rank plot is usually with cell aggregation (multiplets). Partly it could be due to resuspension and chip loading for the first run. The subsequent runs on the same sample may not replicate this issue. However, the data is still usable in such cases. It is also recommended to use Doublet/Multiplet removal methods or remove the ambient RNA contamination from cells using third-party tools.
Related KB articles: Can I remove ambient RNA contamination from cells in my gene expression data?
Products: Single Cell Gene Expression