I've been using TopHat to map my reads and I've received the same error message for the "accepted hits" files for all three of my datasets. I attempted to run the datasets by using the "auto-detect" option but that has so far only worked for one dataset. When I try the same thing for the other two datasets, I receive another error message that reads: "This dataset is currently being used as input or output. You cannot change metadata until the jobs have completed or you have canceled them."
I've cancelled all my jobs after this point in my analysis and to my knowledge I don't think these datasets are currently being used as an input or an output for another job.
Finally, my Cufflinks analysis didn't give FPKM estimates for the dataset that I corrected with auto-detection. According to my workflow in the past, I'm using the same parameters for all my previous analyses so I feel like this problem might be due to the error message I received after I used TopHat.
Please help. The data analysis is very urgent. I really appreciate your help.