Differential expression of miRNAs

Question

[sabaghianamir70]

Hi, I Did a differential expression with the result of MiRDeep2 Mapper process and map reads to a reference genome in galaxy, with salmon and then use Deseq2 for DEG. is this workflow OK ? or im making mistake in calculation. if there is better way can you guys tell me about it. P.s i didnt get any error in this workflow

[ATpoint]

One typically maps short RNA-seq reads against a collection of microRNAs such as miRbase. Reason is that due to the short length one would get plenty of multimappers if aligning against the full genome. Never had to do it myself but the consensus here seems to be bowtie as the tool of choice, which is tailored for very short reads and ungapped alignments.