Scanpy vs DeSeq for single cell RNASeq DE gene analysis

Question

[robert.murphy]

What are the advantages of either in this situation? Scanpy says it is for single cell DE analysis but if I am understandign correctly single cell RNASeq is just the same as any other normal bulk RNASeq but either on a single cell or specific subpopulation of cells?

Answer 1

[ATpoint]

Your understanding of scRNA-seq is quite incomplete if you say that it was the same as RNA-seq. Please get a background first.

Some good reads could be:

https://www.nature.com/articles/s41467-019-12266-7

https://www.embopress.org/doi/10.15252/msb.20188746

https://www.ncbi.nlm.nih.gov/pubmed/29481549

[robert.murphy]

These links are very useful but are all about analysis, I think my misunderstanding is in the differences between bulk RNAseq and scRNAseq. I have previously looked but been unable to find a recourse to inform me on this. However it also appears the main differences are actually in the analysis. but my question still stands and as the wet lab methodology seems to be the same aside for dealing with barcodes to ensure you build a single cell library, so can DESeq be used for scRNAseq analysis?

[ATpoint]

You asked about DESeq so you are asking about analysis. Read the papers. Especially the third one compares (among others) tools such as DESeq2 for scRNA-seq analysis. Yes you can use it but with some modifications. Read paper for details. Also the introduction part of the literature is good to get a background on what separates scRNA-seq from bulk RNA-seq.

[Raz]

in the bulk RNA-seq they compete the average of gene expression over all the cells, while in scRNAseq they get gene expression for each individual single cell.