Mouse miRNA mapping

Question

[AellSidious]

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!

[Asaf]

You're using Bowtie 1 which requires end-to-end alignment, it might not be the best option. Try bowtie2 with --local, you might want to allow a seed mismatch (-N 1).

[AellSidious]

I will try with bowtie2 then. Thank you for the suggestion.