I am using Seurat for scRNA-seq analysis. In the QC step, I found they simply removed the cells with number of gene expressed over 2500 (http://satijalab.org/seurat/pbmc-tutorial.html). Also, when I read this nature paper (Kelley S. Yan et, al 2017), they simply set the cutoff to remove the cells with expressed gene more than 4400 (http://www.nature.com/nature/journal...ture22313.html). I understand it is necessary to remove the cells with low number of genes expressed since they are likely to be dying cells. But I don't understand why peopel remove the cells with high number of genes expressed? It is very possible that these cells are some rare populations. Probably, people may claim the cells are doublets, but is there any evidence for that?
I am building up the QC pipeline for scRNA-seq and eager to know the answer for this. Many thanks in advance!
I am building up the QC pipeline for scRNA-seq and eager to know the answer for this. Many thanks in advance!
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