I have complete mirdeep2 on my 15 samples. Results included several duplicates but the read counts differed. I have done a lot of research but there is nothing concrete on how to handle duplicates and how to cut read counts off that are too low. Once I have that fixed than I need to upload my excel file to R studio but I am not sure how the file should look. I currently have my read counts on 1 tab with the miRNA identified then the next tab has the 15 samples with ID with 3 separate columns of my 3 traits broken into treated or control. I just need some guidance on how to do this process.

If you want to use DESeq2, you should start with the documentation:

Vignette:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

Workflow:

http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

We walk through various ways of importing data in both, but you will need basic familiarity with R to start.