Defining the threshold for reads and features

Question

[zizigolu]

I have some Indrop scRNA-seq

The number of genes per cell and number of read seems like this

Here what I should put to get a good Seurat object?

I have tried this but I think I am missing some cell types

pbmc <- subset(pbmc, subset = nFeature_RNA  1000 & nFeature_RNA < 5000 & percent.mt < 25)

Please look at these plots to give me an intuition which numbers give better results

Answer 1

[jared.andrews07]

Read this chapter of the OSCA book. Nobody is going to be able to tell you hard and fast cutoffs that will just "work". Every experiment is different, as are different cell types. You will have to experiment and find a balance between stringency and retaining potentially real cell populations on your own.

[zizigolu]

Whatever I am trying there is no B cells in the data

How this is possible :(

That is why I am asking for help

I want to know how I can interpret this plot

[jared.andrews07]

I have answers on these metrics here and here.

Regardless, if the cells aren't there (how do you know there aren't any B cells, have you annotated?), then they aren't there.

[zizigolu]

I have used these markers but likely nothing here very weird

>  VlnPlot(pbmc, features = "CD20")
Error in FetchData(object = object, vars = features, slot = slot) : 
  None of the requested variables were found: CD20
>  VlnPlot(pbmc, features = "CD22")
>  VlnPlot(pbmc, features = "CD19")
>  VlnPlot(pbmc, features = "CD79A")
>  VlnPlot(pbmc, features = "CD79B")
>