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Question: No reference transcriptome
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gravatar for wkim
3 months ago by
wkim • 0
wkim • 0 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.
rna-seq genome reference transcriptome • 180 views
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modified 3 months ago by Jennifer Hillman Jackson ♦ 25k • written 3 months ago by wkim • 0
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gravatar for Jennifer Hillman Jackson
3 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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: https://galaxyproject.org/support/

Galaxy Tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 3 months ago by Jennifer Hillman Jackson ♦ 25k
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