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