Hello, I have attempted to upload my h5ad file to MapMyCells with my rows as cluster number and my columns are mice EnsemblIDs. I receive the error: After comparing query data to reference data, no valid marker genes could be found at any level in the taxonomy.
My run ID is 1727674880348-38b484cb-d761-426a-8c26-025f2cf85eb2.
Appreciative of any help with this!
Hi @scaradonna
It looks like you are mapping human data onto the Whole Mouse Brain taxonomy. I say this because the genes in your data are identified with human ENSEMBL IDs (ENSG12345 as opposed to ENSMUSG12345), while the configuration for your job is pointing at the data files for the Whole Mouse Brain taxonomy. Do you agree that this is what you are trying to do?
If so: you will need to create a new h5ad files in which the genes are labeled as mouse orthologs of the human genes. MapMyCells does not yet have the ability to automatically find cross-species gene orthologs. You need to do that before submitting your data to MapMyCells. The science teams at the Allen Institute have provided this GitHub repository to help in finding cross-species gene orthologs.
Does this help?
Sorry: I just noticed where you said “and my columns are mice Ensembl IDs”.
Somehow, the Ensembl IDs in your file actually ended up being for human genes. If you look at the error message, it should say
e=RuntimeError("After comparing query data to reference data, no valid marker genes could be found at any level in the taxonomy.\nExample of genes in query set:\n['ENSG00000039537', 'ENSG00000106804', 'ENSG00000112936', 'ENSG00000113600', 'ENSG00000125730']")
closing with a sample of the gene identifiers in your file (your file is called the “query data”). In this case, those are all human Ensembl IDs (as I said before, mouse Ensembl IDs tend to start with ENSMUSG rather than ENSG).
If you want to see the specific marker genes that we use for mapping to the Whole Mouse Brain taxonomy, you can find instructions for downloading that marker gene table on this page.
Hopefully this is a bit more helpful.