I have RNA-seq libraries from 8 tissues (2 biological replicates for each). I want to determine which transcripts have tissue-specific expression. After I build cufflinks annotations for each of the individual tissues, would it be better to combine them into a single annotation using cuffmerge or cuffcompare? I'm concerned that if only one of the tissues has an assembled transcript at a specific loci, cuffmerge may consider it to not have enough evidence to include. But that's exactly the type of thing I'm interested in finding. Am I misunderstanding how cuffmerge works? It seems like cuffcompare might be better in this situation as it just does a straightforward union of all fragments.