Integration of RNA seq data aligned to different reference genome versions

Question

[susibing]

Hi all,

I would like to integrate a bulk RNA seq and an scRNA seq dataset.

The data was already provided as count matrices, but unfortunately, the bulk RNA seq data was aligned to hg38 whereas the scRNA seq data was aligned to hg19.

Since I have for both the counts for the ENSEMBL IDs, can I still integrate those two datasets or should I preferably re-align to the same reference genome?

Thanks!

[Ram]

It should be trivial to realign. Integrating cross-genome datasets can introduce errors and I think it's worth the realignment effort to eliminate that factor as a possible source of unknown/unforeseeable errors.