I am working with human miRNA-seq data. For alignment, I tried using two tools - BowTie2 and HiSat2 to align the clean reads to the reference genome GRCh38. Interestingly, I observed that HiSat2 provides more unique alignment that Bowtie2. The overall alignment rate was 10-20% higher in case of HiSat2. What might be the possible reason for this? The higher uniquely mapped reads I guess suggests better mapping but I have rarely come across study that uses HiSat2 for the purpose. Also BowTie2 with --very-sensitive-local has been found to be very accurate in mapping miRNA-seq reads (PMC4931105).