Too many reads mapping towards intronic region

[sanush]

Hi all
We just finished our first RNA seq experiment in SOLiD platform and used partek to map our reads. We see that only 30% maps to exonic and remaining of our reads mapping to intronic and intergenic regions (30% on each regions).

We are trying to figure out the reason for high numbers mapping to intronic regions. Any advice.

Thanks

[steven]

FYI, it is not the first time i see some important discrepancy in the proportion of "exonic" reads. For instance 93% (Mortazavi et al), 39% (Li et al, PNAS 2008) or 33% of mapped reads (Tang et al, 2009, Nat.Met).