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


Ateequr Rehman
House No. 2 ground floor
Blauenstr. 10
79115 Freiburg im Breisgau
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