How to get SAM file?

[werhoog]

Thanks for this great software! But I am confused about SAM file. I used bowtie2 to convert RNA-seq fastq files to SAM by mapping fastq files to mm10 genomic index files.However, the unique mapping raito is about 30%! So , am I wrong to map fastq files to genomic index of mm10 to use MISO? What should I do to get SAM files? Many thanks!