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
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
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