No gene symbols

Open hernandezvargash opened this issue 9 months ago • 3 comments

Thanks for this useful tool. I'm trying to visualize my seurat object. I can see my UMAP plot with the reductions I made in R, however I don't gene symbols when I create the project: (100.0%) genes were not found in Ensembl. This happened with .rds .h5ad and .loom formats, also after converting my gene symbols to Ensembl IDs. Thanks for your help!

Apr 15 '25 13:04 hernandezvargash

Hello @hernandezvargash, thanks for your message. Can you please double check that you selected the right species?

Apr 15 '25 13:04 fabdavid

thanks for the fast response, yes, I'm using human gene symbols, they are not recognized when I save my object as an .rds or with SaveH5Seurat + Convert to .h5ad. However, I just realized that I get the gene symbols when I save with SaveLoom(seurat.object). The pipeline works nicely with this loom file.

My problem now is that the loom file did not save my reductions, and I want to keep my harmony integration. Is this actually possible?

Apr 15 '25 14:04 hernandezvargash

Can you please tell me which is the project key or name. I can have a look more precisely like this.

Apr 15 '25 14:04 fabdavid