By bam from outside, I mean the alignment made not by TopHat. Here in Using Cufflinks for RNA-Seq without Tophat/Bowtie. (2.4 years ago), Leszek said TopHat does special splice junction coding for Cufflinks, meaning to me that if the bam files are from something else, RUM in my case, then your Cufflinks run cannot identify the splice junctions.
But at the same time, nobody points out this problem except him and Cufflinks site says they can take in bam/sam files as input. So I am confused. Do you think I can run Cufflinks with a bam files I took from not TopHat?