Detect precursor but not mature miRNA in small RNA-seq data?

Question

[Rey]

Hi all, I am trying to identify known miRNAs. First, I used only mature miRNAs to align with my sRNA-seq data using bowtie. One miRNA is found in one replicate of my library, but not found in another replicate. So, I used both mature and precursor miRNAs together as an input file to find known miRNAs. when I use it, the file containing both mature and precursor miRNAs to align with sRNA-seq data, a precursor of miRNA whose mature was not found, is detected. What I should do? should I use both mature and precursor? If I want to do differential expression analysis, does this affect my outcome?