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Old 07-24-2012, 07:16 AM   #1
Junior Member
Location: Sao Paulo

Join Date: Jun 2012
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Question Differential expression of microRNAs with Cufflinks?

Hello everyone ;-)

I am newbie in RNA-seq analysis and I just want to perform differential expression analysis in microRNA datasets.

I noticed that edgeR and DESeq are widely used for this purpose, instead, I haven't found any work using Cufflinks/Cuffdiff for microRNA differential expression analysis.

As I don't have strong statistics background, is it reliable to perform microRNA differential expression analysis with Cufflinks? What are the drawbacks in such case?

Thank you very much for your help!
Gustavo S. Franša
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Old 07-30-2012, 05:33 PM   #2
Location: St Louis, MO

Join Date: Nov 2009
Posts: 27

Maybe take a look at this paper:

This will get you 'count' data for your microRNAs - I then use DESeq to perform differential gene expression.
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Old 07-30-2012, 05:45 PM   #3
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Location: East Coast, US

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Posts: 177

Hi gufranca,

microRNA analysis is quite different from regular RNA-seq analysis. There are quite a few software packages to choose from:

DZhang is offline   Reply With Quote

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