lncRNA detaction from output cuffcompare or cuffmerge

Question

[yaghoub.amraei]

Hello everyone .. My goal is to identify LncRNA in rice plants. In some articles, they have used the output of cuffcompare or cuffmerge. If we use the output of the cufffmerge, we can only use intergenic LncRNA with class_code (u) and LncRNA on the antisense string (Lnc-NATs) with class_code (x). But in addition to these two code classes, we also have access to the output of the cuffcompare, the intronic RNA with class_code (i) and the overlap Lnc with class_code (o). Which output do you think I should use? thanx