Question: No reference transcriptome
0
gravatar for wkim
3 months ago by
wkim0
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 12 weeks ago by Jennifer Hillman Jackson25k • written 3 months ago by wkim0
0
gravatar for Jennifer Hillman Jackson
12 weeks ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 12 weeks ago by Jennifer Hillman Jackson25k
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