Recommended pipeline for differential miRNA-seq

[AlexClop]

Dear all,

I was a SeqAnswers member few years ago while working on human genetics at Kings' College London. I just re-registered again, in my current job as animal geneticist at CRAG (Barcelona).

We want to carry a microRNA-seq experiment in an Illumina HiSeq2000 to carry a differential expression analysis from porcine sperm.

I would like to know which is the most recommendable bioinformatics pipeline nowadays for our miRNA-seq study.

Thanks for sharing your knowledge and experience!

Alex Clop

[sbarberan]

I use CAP-miRSeq that includes differential expression analysis with edgeR

http://bioinformaticstools.mayo.edu/research/cap-mirseq/