Single cell QC

Question

[parvathi.sudha]

Is there a way to plot the median transcripts per cell, genes per cell, and cell counts for each sample in single cell data? I have integrated 20 samples using Seurat. Trying to check if any sample is an outlier in the integrated dataset.

Thanks Parvathi.

Answer 1

[jared.andrews07]

Please read their vignettes: https://satijalab.org/seurat/articles/pbmc3k_tutorial.html

[parvathi.sudha]

Thank you. But, will this help me to plot the integrated samples (postQC), median reads per cell, genes per cell, and cell counts for all samples in one plot?

[jared.andrews07]

Why would the integrated samples function any differently? You can split the cells up however you'd like by metadata columns. I recommend you read the docs for their VlnPlot function - ?vlnPlot. The group.by parameter is what you'll use to split by sample.

I can also second Friederike's recommendation of dittoSeq, though I have been involved in its development.

[parvathi.sudha]

Okay. One of my sample is having low fraction of reads and low mapping percentage. I am actually trying to compare the filtered cells and features in all the samples to find, if it is really an outlier.

Answer 2

[Friederike]

For plotting, I recommend dittoSeq

[parvathi.sudha]

Thank you.Nice tool to do the celltype comparison.