Stool miRNA – low alignment rate

Hi Guys,

I am having an issue with my miRNA from stool data analysis and maybe you could help me:

Making the alignment with mirdeep2 against the Bos taurus genome we obtained a very low percentage of alignment (5%). Could you tell me if I need to do some filtering before or if I should use another program for alignment?

I’ve already done the mapping against the maize genome and the percentage was also low.

Thanks,
Priscila

You enriched your library with small-RNA? If so, I would check that reads were preprocessed well, miRNA are short so reads will usually contain adapters that must be removed.
You can also try to map directly against the genome, or mirome with mapper like bowtie or BWA to check if things are change.
But I would guess one of the two- either no enrichment for small RNA was done or you need to do preprocessing prior to the alignment