First time poster, sorry in advance for any mistakes.
I have some experience managing RNA seq data for differential expression analysis. I usually follow this pipeline: Pseudoalignment with salmon --> Import counts to R with tximport --> Differential expression analysis with DESeq2
However, I've been asked to do a similar analysis with miRNA seq data and I'm having some trouble with it. The miRNAs were extracted form human peripheral blood and were sequenced with Ilumina technology. I've created an index for salmon with the mature miRBase database and a kmer of 7, as the sequences I'm aligning are very short, and I'm obtaining mapping rates that vary from 1% to 40% for different samples. I don't know why there is such a big difference in the mapping rates. I've tried redoing the index with different kmer values, with the hairpin database instead, changing some parameters in salmon... But the results haven't imporved.
I'm very new to the miRNA world and I haven't been able to find much information about proper miRNA seq analysis. I will be very thankful for any explanation to this problem, recommendation on different tools or how to use salmon for this specific case.