I recently started with Single Cell preprocessing step and I have cells in two batches. Day 16 (control vs Knockout) and Day 40 (control vs Knockout). I plan to use
seurat after preprocessing.
My queries are as follows:
Should I separately apply dropletutils on each control case like
p16C_sce <- read10xCounts(p16C, col.names=TRUE) #dim: 9250 6794880 p16K_sce <- read10xCounts(p16K, col.names=TRUE) #dim: 9250 6794880 p40C_sce <- read10xCounts(p40C, col.names=TRUE) #dim: 9250 6794880 p40K_sce <- read10xCounts(p40K, col.names=TRUE) #dim: 9250 6794880
or should I combine like it has been done here? This is because, when I apply Dropletutils separately, I get
sceobject with different dimensions and I am not sure if that can be ingested by Seurat.
One of my Batch showed ~10% of barcodes with high mitochondrial gene expression, higher than the threshold both in Control and Knockout. Should I retain those cells too because we see similar pattern in both control and knockout?