two species in sample with garnett

[James Hong]

Hi everyone,

I have a complex sample that has both rat and human cells.

So far I've been doing pretty well using monocle3.

The issue is in the cell_data_set and the marker_file, my cell-specific genes are differentiated by hg38__genesymbol (human) and rnor6_genesymbol (rat)

As you might expect, training of the classifier gives an error saying "Not enough training samples for any cell types at root of cell type hierarchy!" but when I do a marker_check this is due to an issue with gene id conversion.

How do I get around this? Would I need to do a find & replace of the species prefixes in the cell_data_set and the marker file?

Thank you

[Hannah Pliner]

Hi,

I think your best bet here is to use the db="none" option and then just match the gene symbols in your marker file with your gene symbols in your cell_data_set. See here: https://cole-trapnell-lab.github.io/garnett/docs_m3/#my-species-doesn-t-have-an-annotationdbi-class-database

Please note that this removes the gene conversion parts of Garnett - so you'll need to add the hg38_ and rnor6_ prefixes to your marker file so it matches the cell_data_set.

Best,

Hannah

[James Hong]

Thank you!

It’s already set up like that, so this is perfect. Will test it.

James 

Sent from my iPhone

On Mar 9, 2020, at 9:40 AM, Hannah Pliner <hpl...@gmail.com> wrote:



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