Question: Problem with data analysis in Galaxy Pipeline (very urgent)
gravatar for sbasu
4 months ago by
sbasu0 wrote:

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.

ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson25k • written 4 months ago by sbasu0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:


There were some problems with Tophat earlier and those are likely corrected by now (post job metadata assignment). To change/correct metadata, the jobs involving that dataset need to either complete or be permanently deleted and then cleared from the server (if the job was executing already, it will take longer to clear).

For the Cufflinks issue with FPKM, review the input Tophat BAM dataset first to make sure it actually contains hits and not just a header. Then double check that any reference annotation used is an exact match for the reference genome mapped against. The FAQs here cover the most common issues when this type of problem comes up: -- start with the first one.

That said, Tophat and all Cuff tools are considered deprecated at this point and are lower priority tools to maintain on the public servers. We strongly recommend that you upgrade to using the latest tools and methods for RNA-seq analysis. Many examples are covered here:

If you really need to use Tophat, Cufflinks, and other older tools -- then moving to your own Galaxy server (local, docker, cloud) where you can control the exact environment to replicate an analysis would be a good strategy. All of these can impact reproducibility: the Galaxy version, tool versions, data versions, compute resources. All prior releases of Galaxy and wrapped tools are available. Please see:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson25k
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