I have two single-cell datasets: one from mouse and one external human dataset. I want to integrate these two datasets using the SCTransform workflow. I am also planning to try other integration methods, but I chose SCTransform because it works well with my mouse samples.
To align the genes between mouse and human, I am using an orthologs table to match the genes. However, I wanted to confirm if this approach is appropriate or if there is a better method for integrating mouse and human data.
I came across a paper (https://www.nature.com/articles/s41467-023-41855-w) that benchmarks different integration methods across species. However, this study did not test the SCTransform workflow and did not exclusively integrate mouse and human datasets. I was wondering if anyone has experience with a similar integration or can offer insights into the best practices for cross-species single-cell integration.
I appreciate any suggestions. Thank you!
