correlation between SCRNA-Seq and bulk RNAseq
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3.5 years ago
kanwarjag ★ 1.2k

I have selected 1800 cells and 1600 genes from scRNAseq (Single cell RNASeq). I have a public data set of bulk RNAseq of 5 replicates. If I want to show correlation in expression of scRNA and bulk RNA seq what should be the best way to show in a figure. I can simply calculate the average expression of each genes in ScRNA Seq and bulk and calculate pearson correlation coefficient but could not figure out how can a draw a figure from this information. Any alternative method suggestion is also welcome. Thanks

RNA-Seq • 3.9k views
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Entering edit mode
3.5 years ago

You are on the right path: You need to plot the expression values of genes in scRNA vs Bulk and as a scatterplot. And then give Pearson correlation (or R^2) as an indication of the correlation. You might need to remove the low-counts reads from either side because they are usually noisy. See Figure 1h for an inspiration

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191988/

And somebody already did many comparisons: https://jdblischak.github.io/singlecell-qtl/sc-vs-bulk.html

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