I'm trying to map some mouse (mus musculus) miRNA reads on reference mature miRNA sequences from miRBase with Bowtie.
Problem is that the percentage of aligned reads is very low, between 1% and 5%.
Here the bowtie parameters I used:
-n 1 -l 10 -k 1 -m 1 --best --strata
Any idea on how I could improve the alignment?
Thank you in advance!