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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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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