TobiTekath
commented
5 months ago 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.
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