Hey all. I've finally managed to get my local instance of Galaxy mostly up and running. However, I'm having a problem getting Cuffdiff to work locally. Specifically, when I supply it with my accepted hits from tophat, and with a reference annotation (.gtf) from iGenomes, I get the following error, "Error: sort order of reads in BAMs must be the same." When I run Cuffdiff with the exact same files on the public server, it runs just fine. So, I'm guessing I might be missing something from my local instance? I've got Samtools installed, but not sure if I need to add something else for Cuffdiff to work. Any help is greatly appreciated.
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