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
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