Hello everybody,

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!