I have a microRNA seq data (RNA seq after depletion of rRNA) using Illumina TruSeq Small RNA kit. Once I have the FASTq files as out put shoudl I be aligning to genome (suh as hg19) and than map the miRNA from a bed file from any mirRNA db or alternatively just align to mirRNA db.IS there an speific aligner to align to miRNA db or only blast is the option. What should be the best/ traditional approach.
Thanks