differential expression analysis of microrna generated by NGS platform

[vcc]

Hi all,
I am very much new to this NGS technology. I have already used cufflinks for transcriptome analysis as a small project. But now I am looking to get differential expression analysis of microRNA single ended reads. So my question is will it be reasonable to use cufflinks on this data too?
If not so, kindly can I get some explanation for the same.

Hoping to get response soon.

thanks all.

[Xiaomin Yu]

You could try cuffdiff if you make your own miRNA gtf file, or you can use miRdeep2

[gpcr]

How to use mirdeep2 for differential expression analysis

1. How can i use mirdeep2 outputs for differential expression analysis?

2. which files to use? results.csv or expression.csv?

3. how to deal with duplicate mature miRNA(with different precursors?) in the output.

thanks for your inputs.