Hi,

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 exon?

Thanks