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
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