[BioC] mirDeep2 edgeR analysis

Ryan C. Thompson rct at thompsonclan.org
Tue Aug 20 22:03:04 CEST 2013

Hi Mariana,

As a first attempt, it would seem that the most straightforward thing 
to do is to count the reads in each sample mapping to each miRNA and 
then analyze those counts as you normally would using edgeR. In other 
words, just treat it like RNA-seq data. If that doesn't work, then 
you'll need to get more creative, but that should be a good start.


On Tue 20 Aug 2013 07:01:05 AM PDT, Flores Torres, Mariana wrote:
> Hello,
> I wondered if anyone has experience with microRNA seq data analysis??
> I have miRNA sequencing data from Illumina (control vs treatment) and have used mirdeep2 for analysis (it uses bowtie to aligne to miRBase) but I'm not sure how to perform differential expression, hope someone could please guide me through this!
> Many thanks!
> Mariana
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