# What is the best way to map/align my reads on a given genome?

I am frequently using a ballgown package for my rnaseq analysis, but recently I have had a new task to have my reads mapped on two different genomes to understand the level of alignment between the two, therefore I wonder what is the best tool to do this? I have single-end reads. What I need is to have a percentage of uniquely mapped fragments, mapped to multiple loci and, say, unmapped. Can bowtie do the job? Is there a standard explanation procedure explained elsewhere? Thanks.