Generate short-reads for RNA-Seq.

[wilson90]

Hi,

I would like to generate short reads for RNA-Seq based on GTF annotations. However, I notice the difference in the strand of exons (i.e. some maybe + strand, or - strand) My question would be:

Does it matter if I ignore the strand information and generate reads without considering the strand information?

Example

Exon 1: ATGGGGGG ("-strand")
Do I generate short reads with this sequence "ATGGGGG" or "TACCCCCC"?

Thank you.
Does it affect my mapping using Tophat?