Question: Add Reference Genome When Designing A Workflow
gravatar for marcuslevitt
2.7 years ago by
marcuslevitt0 wrote:

Hello Scientists,

I have been running my workflow manually and when I use CuffLinks and CuffDiff I have been performing bias correction, to which the software automatically assigns the hg19 random chrM HapMap, which I believe to be the correct file.

However, I have now designed an automatic workflow and when I come to run the workflow with fastq files I cannot assign reference genome to the bias correction stage at both the CuffLinks and CuffDiff stage.

Would I have to add the HapMap as a separate file? If so do you have a link to save the Hapmap?

Many Thanks

Struggling Undergraduate

ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by marcuslevitt0
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This tool option must be selected inside of the workflow and saved for it to be active on the Execute Workflow form (center panel when a workflow is selected for use). On that form, you can modify the target reference genome at run-time for most tools. Pick the same one as used for mapping.

Also, make certain that the input files have the "database" metadata assigned. This includes the HapMap reference genome. This permits the tool to recognize the inputs. There are some internal data checks that help with usage to ensure that all inputs are based on the same exact reference genome, based on the database assignment. I suspect you are using a custom reference genome? Create a custom reference "build" to use this as a "database".

If this continues to be problematic, let us know and we can follow up, likely by asking you to send in a shared link to the history and workflow for feedback (if this can be replicated at But the above is what we would check and doing this yourself is quicker.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Jennifer Hillman Jackson25k
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