Hi; I have a list of transcripts with tag counts for each of them in 8 different tissues. My list includes many isoforms of similar genes etc. which is not a problem for me - but will it effect the stats from edger as obviously some tags are counted multiple times. There are 40M tags in each experiment so I am assuming the aggregate effect should prevent any great problems. My main questions are; 1. I would like to identify which transcripts appear to be specific to an individual tissue from my 8 2. Which genes are ubiquitously expressed across all 8 Cheers Dennis [[alternative HTML version deleted]]