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.
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parvathi.sudha •
Please read their vignettes: https://satijalab.org/seurat/articles/pbmc3k_tutorial.html
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?
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.
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.
For plotting, I recommend dittoSeq
Thank you.Nice tool to do the celltype comparison.
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