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?