subsetting seurat object with multiple samples

Question

[Assa Yeroslaviz]

I have a seurat object with 10 samples (5 in duplicates). I have added them all together and created the VlnPlot to check for the quality of the samples.

As one can see in the pic below, the quality is quite different in each of the duplicated conditions. I was wondering, if it make more sense to find subsetting parameters which will comply with all the samples, or one can do it one sample (or one condition) at a time by itself.

What is the best way to proceed?

thanks

Answer 1

[jared.andrews07]

Generally, you'll want use different parameters for each sample. But even then, using a blanket threshold for all clusters in a sample may remove populations of biological interest. A recent question here gets into that particular problem a bit.

As an aside, your middle two samples with a majority portion of cells with %mitochondrial reads > 10% are rather worrying, as they may largely be dead/dying.