Annotate the mouse scRNA data

[yangfeizZZ]

Hello
Thank you for your tools.It's very good.But i don't how to use it to annotation the mouse data.
I hope you can reply as soon as possibile. Thank you!

Best wish!

[Zha0rong]

Hi @yangfeizZZ ,
I think in this case what you can do is to make a xlsx file which included mouse gene markers for mouse cell types.

Next, let's prepare gene sets from the input cell marker file. By default, we use our in-built cell marker DB, however, feel free to use your own data. Just prepare an input XLSX file in the same format as our DB file. DB file should contain four columns (tissueType - tissue type, cellName - cell type, geneSymbolmore1 - positive marker genes, geneSymbolmore2 - marker genes not expected to be expressed by a cell type)

[shaniAmare]

Hi @yangfeizZZ , I think in this case what you can do is to make a xlsx file which included mouse gene markers for mouse cell types.

Next, let's prepare gene sets from the input cell marker file. By default, we use our in-built cell marker DB, however, feel free to use your own data. Just prepare an input XLSX file in the same format as our DB file. DB file should contain four columns (tissueType - tissue type, cellName - cell type, geneSymbolmore1 - positive marker genes, geneSymbolmore2 - marker genes not expected to be expressed by a cell type)

Hi,

I think this actually will not work as there is a checkGeneSymbol function running within the gene_sets_prepare.R script which checks for the genes to be on human gene symbol pattern. It would be an easy fix to change this to look for mouse genes and I'll try to create a pull request for that if I get time. But according to the package HGNChelper authors (which the above checkGeneSymbol function comes from) the mouse annotations are invcomplete. So there could be some downstream unexpected problems.

Therefore, as of now, there is no solution to this other than to consider them as human genes and run the script.

HTH,
Shani.