After mapping RNA-Seq paired end reads with Tophat,  I can see that most of 
reads fall into the right regions. However, I still can see lots of reads 
mapped to non-coding region (the locations where the reads are mapped to don't 
contain exons). 

I am wondering if these "non-coding reads" will be included when cufflinks 
calculates transcript/gene expression.
Dying to know your opinion.

And another question is:  how to know the number of reads mapped to a certain 

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