Scanpy analysis for a combined species. I have tried following the normal pipeline to work with the data, but it fails to find MT/mt genes in single cell dataset aligned to both mouse & human genes.

[echoo07]

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the master branch of scanpy.

---

Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.

Minimal code sample (that we can copy&paste without having any data)

# Your code here

[Paste the error output produced by the above code here]

Versions

Details

[Paste the output of scanpy.logging.print_versions() leaving a blank line after the details tag]

[LuckyMD]

I guess you probably converted all of your gene names to the genes from 1 specie to be able to put them in the same anndata object, no? In that case your problem is solved. Otherwise, I would recommend to at least harmonize the mitochondrial gene names to run this analysis.

[echoo07]

Hi thank you so much for you reply. Initially I didn't understand your former statement, but looking at the features table, I understand what you mean now, it's strange that cellranger mixed species alignment adds mm10 or GRCh38 infront of the gene symbols as well which wasn't letting it find the mito-genes on following the scanpy pipeline at the pre-filtering mito genes steps.


.

[LuckyMD]

I'm glad you found the issue then! I do understand why this is prefixed though... it would be quite confusing having a data object with mixed genes from mice and humans and this not immediately being obvious. I often catch myself looking up which specie was capitalized and which wasn't ;).

[LuckyMD]

Can this issue then be closed?

[Zethson]

Glad you figured it out and thanks @LuckyMD for helping out.

In any case, please ask usage questions here: https://discourse.scverse.org/