Is it possible to use cytotrace2 for snRNA-seq data?

[Tailion9]

Thanks for the great tool!

I was using it for single-nuclei RNA-seq dataset but found low CytoTRACE2_Scores (< 0.2) output for every batch.

I wonder if this is because of the poor quality of my snRNA-seq dataset or it's a more general condition. I found it really difficult to use CytoTRACE2 scores for development root prediction for my snRNA & scRNA combined dataset.

Here's my cluster result for this combined dataset, with batch effect corrected:

And the CytoTRACE2 scores for every cluster, which was computed for every batch as instructed:

[savagyan00]

Hello and sorry for the delayed response,

Single-nucleus RNA-seq data generally tends to have lower UMI/gene counts than single-cell RNA-seq data. While generally insensitive to variation in gene/UMI counts per cell, CytoTRACE 2 requires further optimization for cells that have exceedingly low gene expression levels, particularly those with fewer than 500 genes expressed per cell, as its performance can become less reliable in these cases. For best results, a minimum gene count of 500-1000 per cell is recommended.

So I would suggest checking if your snRNA-seq cells contain very low counts. You can also try the latest release of the tool (v1.1.0) which has significant performance enhancements and also does an internal check for the fraction of cells that do not meet the minimum recommended counts threshold.

Please let us know if we can help with anything.