I'm working with a data set with 8 samples and have run them through bow tie (previously) and am trying to run them in cufflinks now. The odd numbered samples I have run fine and produce data but the even numbered samples I have all produce no data in terms of an FPKM or any other calculation. I'm looking at gene expression and my test samples are in fact the even numbered ones that are not providing me with calculations. Is there a simple reason for this? Apologies if this is a simple question but I have tried to adjust the settings a few time to no avail. Any and all help would be greatly appreciated. Thanks!