I have some SAM/BAM files containing the alignments of small RNA-seq reads to mm9 that are created by BWA. I'm interested in calculating where they are mapped to in the genome. I noticed that there are a lot of reads that are mapped to multiple loci (multi-mappers) in genome. Therefore, I first separated the unique-mappers from multi-mappers and counted intervals of unique-mappers overlapping different regions of the genome using the bedtool in the galaxy. Now here comes the issue: as multi-mappers are mapped non-uniquely to various regions in the genome, if I simply use the same method as the uniquely-mappers, I will overestimate the number of counts, how can I count the normalized intervals of multi-mappers overlapping different regions of the genome? Is there any tool in the galaxy or R package that I can use? Thank you for your help in advance!