I've short RNA reads (18-47 nt). I want to perform the alignment, for that I've two questions: 1- Can I use STAR to perform the alignment ? if no, what alignment program do you recommend me ? 2- Shall I align the reads against the reference genome (for example Homo_sapiens.GRCh38.dna.primary_assembly.fa), or It is recommended to include other databases for miRNAs (miRBase) for example ?
Thanks in advance