Off topic:Read Alignment In Rna Seq

Question

[Shivani Grover]

I was wondering that we we align reads to the Reference genome, multiple reads might map to the same stretch of sequence. Multiple reads in one position means that stretch of sequence is important and is expressed more in the transcriptome. But, is there any cut-off as to how many minimum reads should align to a stretch of sequence before we classify it as over expressed. How do i calculate that cutoff. I use Tophat to align the reads and then use cufflinks to study expression.

Thanks