scRNA sequence compare between conditions and get differentially expressed genes

Question

[orzrzlyo]

Hi, I'm very new to Bioinformatics and this might be a silly question.

I'm tending to compare two conditions(control, treatment) of scRNA seq (features.tsv.gz, barcodes.tsv.gz, matrix)
so, i will be having total of 6 files. (two of each features, barcodes, matrix file).

I was able to open and normalize, PCA through Seurat package from R.

Is it possible to compare the conditions (control, treatment) and get the differentially expressed genes between them?

Please let me know.

Thank you

• I'm looking at the data in GSE129218

Answer 1

[fracarb8]

Assuming you seurat object is called mySrtObject and that you have a column in the metadata (e.g. [e-mail]$condition) in which each cell (row) is label as either control or treatment, you can:

Idents(mySrtObject) <- "condition"
id1 <- "treatment"
id2 <- "control"
degMarkers <- FindMarkers(mySrtObject, ident.1 = id1, ident.2 = id2)

You can read more about it in the seurat base tutorial.