Add_Mito_Ribo multiple species

Question

Add_Mito_Ribo multiple species

Closed this issue 5 months ago · 3 comments

Hi and thanks for writing this incredibly valuable package! I'm wondering if it would be possible to add an option to Add_Mito_Ribo to use multiple standard species? I want to use both mouse and human. Thanks!

Answer 1 · 2024-05-09T15:56:18.000Z

Hi @rhart604,

Yes, that should be possible with some tweaks. Just to clarify this is in case that you have dataset aligned to a combination genome both mouse and human in same dataset correct?

Best,
Sam

Answer 2 · 2024-05-09T16:01:56.000Z

Yes. A standard 10X reference for a mixed mouse/human run uses "hg19-" and "mm10-" prefixes for gene symbols.

Answer 3 · 2024-05-09T20:10:36.000Z

Hi @rhart604,

Ok this is now live in the release prep branch "release/2.2.0" (v2.1.2.9061 or greater). To run use following (and replace species_prefix as needed):

OBJ <- Add_Mito_Ribo(object = OBJ, species = c("mouse", "human"), species_prefix = c("GRCm39-", "GRCh38-"))

Note: the order of species and species_prefix parameters MUST match or function will fail to find any features.

If you have any issues with the function after updating to in dev branch please let me know and I'll reopen the issue.

Best,
Sam