Question

RNA Seq analysis vs. Single cell RNA seq analysis

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fawazfebin ▴ 60

@fawazfebin-14053

Last seen 4.7 years ago

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?

rnaseq scrnaseq edger • 1.8k views

ADD COMMENT • link 7.5 years ago • updated 7.4 years ago fawazfebin ▴ 60

score 2 · Answer 1 · 2017-10-06

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James W. MacDonald 68k

@james-w-macdonald-5106

Last seen 8 hours ago

United States

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 COMMENT • link 7.5 years ago James W. MacDonald 68k

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Ok. Thanks for the guidance.

ADD REPLY • link 7.5 years ago fawazfebin ▴ 60

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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 REPLY • link 7.5 years ago Gordon Smyth 52k

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Another relevant paper:

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

ADD REPLY • link 7.5 years ago davide risso ▴ 980

score 0 · Answer 2 · 2017-11-05

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fawazfebin ▴ 60

@fawazfebin-14053

Last seen 4.7 years ago

Great thanks !

ADD COMMENT • link 7.4 years ago fawazfebin ▴ 60