how to filter out cell after doing QC I was wondering that the threshold that we set after doing QC in Seurat. there is an example

# GenePlot is typically used to visualize gene-gene relationships, but can be used for anything 
# calculated by the object, i.e. columns in object@meta.data, PC scores etc.
# Since there is a rare subset of cells with an outlier level of high mitochondrial percentage
# and also low UMI content, we filter these as well
par(mfrow = c(1, 2))
GenePlot(object = pbmc, gene1 = "nUMI", gene2 = "percent.mito")
GenePlot(object = pbmc, gene1 = "nUMI", gene2 = "nGene")`




Then its filter cell command is under:

# We filter out cells that have unique gene counts over 2,500 or less than 200
# Note that low.thresholds and high.thresholds are used to define a 'gate'
# -Inf and Inf should be used if you don't want a lower or upper threshold.
pbmc &lt;- FilterCells(object = pbmc, subset.names = c("nGene", "percent.mito"), low.thresholds = c(200, -Inf), high.thresholds = c(2500, 0.05))` 


So I want to know whether the threshold setting is depending on the picture I show?

And the below is the Geneplot I have got base on my data. How can I set my thresholds?
Yes, you end up placing filters where things become inconsistent or similar to background. In the example, which appears to be from the Seurat tutorial, there's a downward plunge in nGenes vs. nUMI at around 200 genes and few believable cells with more than 2000-2500 genes, so the tutorials sets filters around there. The 0.05 mitochondrial contamination is a more arbitrary round number and is less supported by the plots (one would use more like 0.06 or 0.07 if one based this solely on the plots).