I am using bowtie2 on galaxy to map ChIP-seq single end and paired end libraries to a reference genome. I want to be sure I get only uniquely mapped reads (for single end) or uniquely mapped paired of reads (for paired end). I don't want : reads mapping at multiple locations and being randomly assigned a location; reads mapping to multiple locations and being assigned all the locations. I really want proper uniquely mapping reads. And I need it because I am working with repeated sequences (I saw some posts that suggest we shouldn't care about multimapping but in my case, is kinda of important) Is this possible with bowtie2? I couldn't find it in the manual but again, I am not an expert.