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.
for details.
J.