Non uniform gene coverage and Cufflinks predictions : artifacts ?

[hugo D]

Dear all
We are studying a 1500bp gene. Cufflinks on RNA-seq from 2 different biological groups predicts 3 splice forms: one full-length one and two shortened :


Maq mapping of reads confirms higher expression at the 5' and 3' ends. This supports Cufflink's predictions.
first biological group :

second biological group :


However, no reads indicate polyadenylation of the the 3' end of first short splice form.
Thus we wonder if the 2 short splice forms are artifacts.
Any ideas what may be going on?

hugo