I'm working with a single nucleus RNAseq dataset generated via 10X. I've got 8x samples, which usually I'd run individually through cellranger and merge with Seurat. However, in this case at least some of the samples we expect that in addition to mouse cells, we will also have cells from a human source. Some searching has led to the use of kallisto bustools for mixed species single cell, in particular this tutorial that I've been attempting to follow. I've run this through and I'm getting an output that seems to make sense in terms of cell numbers - but, the matrix output doesn't allow to distinguish which droplet came from which sample, which is vital for this study.
The mixed species tutorial suggests that
kallisto bus can handle multiple samples (coincidentally they also use 8 samples in the tutorial), but the manual doesn't list an option to keep the sample ID data. This separate bustools tutorial suggests that it might be a case of running
kallisto bus for each sample, then aggregating the count matrices afterwards. Does anyone know if that is indeed the case, or am I missing something?
Thanks in advance.
Thanks @dsull. Inevitably just after I posted, I found that cellranger can also take a custom reference constructed from multiple species, so that adds another option into the mix.
I think the approach you suggest sounds reasonable though:
I will see how this goes, thank you again!