I am working on integrating multiple datasets together across a few species. Some are datasets that I've collected, and some are publicly available. Because of this, the sequencing saturation is going to be different for the different datasets, and I'm not sure how that will affect the integration as well as downstream analysis.
Does anyone know:
1) Does Seurat rPCA integration take differences sequencing saturation into account?
2) Is it necessary to downsample such that all datasets have the same reads/cell? If so, how would I go about doing this?
I am working on integrating multiple datasets together across a few species. Some are datasets that I've collected, and some are publicly available. Because of this, the sequencing saturation is going to be different for the different datasets, and I'm not sure how that will affect the integration as well as downstream analysis.
Does anyone know: 1) Does Seurat rPCA integration take differences sequencing saturation into account? 2) Is it necessary to downsample such that all datasets have the same reads/cell? If so, how would I go about doing this?
Thanks!