I am using Bowtie2, and it always maps my reads to multiple locations, which is problem for me. I need each read to be mapped to only one location (by using best from available score). Manual is saying that Bowtie2 maps 1 read to 1 location by default. Which is not true. Please, could you help me to solve this problem?
What's the command line you're using to perform alignments? I say this because if you specify the -k option, then bowtie2 will look for multiple valid alignments for your reads.