I am attempting to run Cufflinks on Galaxy main to analyze my E. coli RNAseq data. I have mapped my reads using an outside program (Genious) and uploaded the resulting BAM file. I also have uploaded the E. coli annotations as a gtf file. However when I attempt to run Cufflinks using my annotations it just stays on "Job is waiting to run" for hours. If I click on "Edit attributes", I see an error message "Required metadata values are missing". Does this mean that my files are somehow incomplete and cufflinks will never run, or do I just need to wait longer? When searching around the mailing lists I saw others have had issues with bacteria due to its circular chromosome, and was wondering if this might somehow be related. Thanks.
Rachel
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