Question: No reference transcriptome
gravatar for wkim
3 months ago by
wkim0 wrote:

I wish to perform RNAseq analysis and some of the alignment algoritms (kallisto, stringtie etc.) do not appear to be showing options for reference transcriptome.

There is the following message;

"If your transcriptome of interest is not listed, contact your Galaxy administrator"

Please let me know how to access the referece transcriptome.

ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by wkim0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Most tools do not include reference transcriptomes. Instead, set the option to "Use a transcriptome from the history".

You'll need to locate, upload, and ensure proper formatting for your Custom Transcriptome. The process is the same as when preparing a Custom Genome. Or, sometimes it is more appropriate to create one yourself within Galaxy (example: with Trinity).

If you are using reference annotation in your analysis, that needs to be a match for your transcriptome. The FAQs below explain the technical procedures and the Galaxy Tutorials have RNA-seq scientific analysis example workflows.

Support FAQ:

Galaxy Tutorials:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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