[galaxy-user] Help!! Tophat paired end reads

Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation.

I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map these reads. After mapping, I used IGV to have a look at the mapping.

I can see that some of the reads fall into exons or span exons (splice junction). These reads seem to fit very well. However, I can also see a lot reads mapped to non-coding region. Are these reads from pre-mRNA? or my mapping was wrong? Did anybody have similar experience??

Furthermore, I can see huge enrichment of reads in 3' UTR (much much more than the coding region). Is this normal? Is this caused by the rRNA depletion method ?

Looking forward to your reply Jiwen