Hello,
I am working on some single-cell RNA-Seq samples and wondering what the difference between a typical RNA-Seq analysis and single-cell RNA-Seq analysis is?
Can we use standard Subread and DESeq2 pipeline to work with the data?
#scRNAseq #RNAseq #singelcell
Thank you
Dear Arash
In RNA seq, typically RNA is extracted from a tissue which may have several cell-types. As a consequence at the time of RNAseq analysis we do perform analysis which is not cell-type specific! Therefore depends on the tissue sampling, results of RNAseq might not be comparable across experiments.
Single -cell has overcome this problem. Before RNAseq, cell would be sorted then RNAseq will be performed on specific cell types separately. Then analysis will be done based on several cell types. The data is much larger than conventional RNAseq and analysis requires a very stronger specs.
Further details can be found at: https://www.10xgenomics.com/single-cell-technology/
The main difference between scRNA-seq and standard RNA-seq is (A) a bit more complicated analysis workflow and (B) often different goals.
The additions to the normal analysis in scRNA-seq include handling cell and UMI barcodes throughout the process so you can reach a reliable matrix of values per-cell. This assumes you're using an scRNA-seq method that uses UMIs, of course. Aside from that you can mostly use the same tools. salmon and a lot of other tools now provide options to better handle quantification of scRNA-seq data (i.e., they now make it easier), so take advantage of these options if you can.
There's often a difference in goal between the two sets of methods. Bulk RNA-seq is typically used to assess changes due to experimental conditions, whereas scRNA-seq is more frequently used to assess differences between cell types (or to find cell types). You can assess changes due to an experimental condition in scRNA-seq too, of course, though it's a bit more involved since you need to identify cell types for comparison across samples.
This tutorial will help you to understand a bit more of scRNAseq and the differences for bulk RNAseq:
https://scrnaseq-course.cog.sanger.ac.uk/website/introduction-to-single-cell-rna-seq.html
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