I have used mirdeep2 for a basic analysis of differential expression between samples, but I am curious as to whether this software can be used to look at differences in non-templated nucleotides on the ends of miRNAs. I trimmed the reads, etc. using mirdeep2 tools and then I did the bowtie alignment to the genome myself, changing the default parameters to allow more mismatches at the ends. However (do I understand this correctly from the paper?), the quantifier module doesn't use the alignment to the genome but rather redoes the alignments to just the miRNA sequences. In the quantifier module it seems like you can change the number of mismatches it allows at this step but you can't specify that the mismatches ought to be at the end, the way you can with actual bowtie.
Is there a recommended workflow for looking at differences in non-templated nucleotides on miRNA ends? Is there some way to use mirdeep2 to do this, since I am familiar with this software?