How to import .mtx files?

[vasikara17]

Hello, thanks for the great tool! I am having trouble using the type of matrix I have since the method I am using for single cell is a bit different. The alignment is done with STAR and I have as an output a DGE.mtx file, which I use in Seurat analysis. Is it possible to use it as an input in your package?.

I have done the Seurat analysis and used the section in your vignette which says starting from the Seurat object but the combine_to_matrix should be done if I understood correctly.

Do you have a suggestion on how to solve this?

Many thanks, Vasiliki

[TobiTekath]

Hi @vasikara17,

you can surely use your gene-level(?) STAR counts with DTUrtle's DGE analysis - and if you already have the data imported into an Seurat object it is even easier. Just provide the object to run_deseq2(), providing your seurat object as the counts parameter, and the Seurat objects meta.data table as pd.

Please make sure that the Seurat object's active.assay contains raw and unscaled count information - most probably it should be the "RNA" assay.