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Question: RNA Seq analysis vs. Single cell RNA seq analysis
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gravatar for fawazfebin
12 months ago by
fawazfebin30
fawazfebin30 wrote:
Hi I would like to know how similar is scRNA Seq analysis to normal RNA seq analysis. What are the additional steps to be followed in scRNA Seq analysis, especially during differential expression step?
ADD COMMENTlink modified 11 months ago • written 12 months ago by fawazfebin30
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gravatar for James W. MacDonald
12 months ago by
United States
James W. MacDonald48k wrote:

They aren't very similar at all. That said, this support site is intended to help people with specific questions about Bioconductor packages, not as a source of generalized knowledge about various analysis methods. There are any number of manuscripts and blog posts as well as vignettes for the various Bioconductor packages that are dedicated to scRNA. You might start by reading some of those.

ADD COMMENTlink written 12 months ago by James W. MacDonald48k
Ok. Thanks for the guidance.
ADD REPLYlink written 12 months ago by fawazfebin30
1

This would a good place to start: https://www.biorxiv.org/content/early/2017/05/28/143289

Initial publications on scRNA-seq assumed that DE methods developed for bulk RNA-seq would not work well. More recent comparison studies have tended to show that, when applied in an appropriate ways, for example with reasonably strong appropriate filtering, bulk RNA-seq DE methods perform relatively well on scRNA-seq data.

ADD REPLYlink modified 12 months ago • written 12 months ago by Gordon Smyth35k
1

Another relevant paper:

https://www.biorxiv.org/content/early/2017/06/30/157982

ADD REPLYlink written 12 months ago by davide risso750
0
gravatar for fawazfebin
11 months ago by
fawazfebin30
fawazfebin30 wrote:

Great thanks !

ADD COMMENTlink written 11 months ago by fawazfebin30
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