[galaxy-user] Cuffdiff

Dear All I have simple and question for cuffdiff should we run cuffdif on merge transcript file (produced by cuffmerge) and concatenate data sets or directly on cufflink produced files, in the later case, i have two transcript files resulting from cufflink on sample 1 and 2 respectively, result using sample 1 as transcripts are not the same when i am suing sample 2 as transcript i am bit confused what should be the correct way any help is very much welcomed Best ateeq   Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau