I want to use DESeq2 for analyze my miRNA data. In the vignette from DESeq2 I didn't quite understand which input file we should use for Differential Expression (DE) analysis. I processed my data using miRDeep2, now I need to use DESeq2 to do the DE. Is there any step before DESeq2? Can I go from miRDeep2 results straight to DESeq2?

You need a numeric matrix of raw counts, typically integers with rows being genes and columns being the samples. With this you can build your DeSeqDataSet as described in the manual. For more help please add details where you get stuck.