> 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
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.
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