> I am wondering if these "non-coding reads" will be included when cufflinks 
> calculates transcript/gene expression. 

Reads will only be included if they map to assembled/known transcripts.

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

This isn't possible because a single read may map to multiple exons and/or 
transcripts. Cufflinks assigns reads probabilistically when their mapping 
cannot be uniquely determined.

See

http://cufflinks.cbcb.umd.edu/faq.html#count
http://cufflinks.cbcb.umd.edu/howitworks.html

for details.

Best,
J.
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