9.8 years ago by
I would recommend to map to the genome first. The reason is two-fold: first, many reads that can potentially map to microRNAs also map to other regions of the genome, and therefore should be discarded; second, this permits the detection of new microRNAs not described in miRBase (which can be very useful if you species has not a comprehensive catalog).
If you're working with a well studied species, such as Drosophila or human, the quickest way is to map to miRBase directly.
For mapping in base-space, Bowtie works great. You should remove first the linkers from your reads. However, since linkers can also have mismatches, I recommend you to trim one-by-one nucleotide at the 3' end sequentially before mapping. This is a personal choice, though, but it worked quite well for us. You may find more information about this procedure in:
Hope this helps!