Im working with a scRNA data set and trying out some different filtering parameters other than using the Seurat vignettes. Specifically I am working at plotting metrics like count depth/cell and genes/cell. Im using this paper as a guide.
I plotted a histogram of counts per cell from my count matrix and got the these charts of the whole population and also zoomed in on the first 4000 counts/cells
My questions were:
1) What do the two peaks represent in this dataset/why are there two peaks
2) Based on the data from the zoomed in histogram, it looks like there's a drop at 900 before it starts to go up again. Should I filter out all counts/cell > 900 (or 1000)?
Thanks in advance!
Edit: Here is another plot of genes/cell from a different data set; why the low peak, then the high peak? What should be filtered from this set, should the filter be set at 300 or after the first small peak?
Would anyone be willing to provide insight from these histogram results?