I have a quick question. I am trying to merge my cufflinks. I have 2 different groups and 3 replicates each, totally 6 cufflinks. I also have a reference gene file (GTF). Could you tell me how to dispose of these files? when I select files for merge should I use 'multiple datasets' or 'insert additional GTF'. Please let me know how to handle them.
Thank you for your help in advance.