My dataset contains a number of smallRNAs and after alignment using bowtie with the non-coding region of the human genome (most recent version of HG 38) only 51% was aligned. I was wondering if I should maybe grep for example miRNA and piRNA first and align them to miRBase and piRbase respectfully. Then align those that remain to the non-coding region of the genome? Or is there another way I could improve alignment score?
Any suggestions or help is greatly appreciated!