How to make volcano plot

workflow
#1

Now I’m trying to create volcano plot from the test data.
I’ve followed the galaxy training tutorial (https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.html#create-volcano-plot-labelling-genes-of-interest) and successfully inputed the test data, but I can’t find out where the “Volcano Plot” bouton is in the Galaxy page.
Sorry for this easy question but it would be grateful if could help me.

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#2

use Limma. it gives you volcano .

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#3

Hello,

Find the Volcano Plot tool at Galaxy EU https://usegalaxy.eu.

It is not installed at Galaxy Main https://usegalaxy.org. But, I’ll review and see if we can get it added in (won’t be immediately, even if Ok’d).

Using Limma as @amir suggests is also an option for RNA-seq.

Please be aware that not all tools in all GTN tutorials will be hosted at the different Galaxy servers. Reference:

#4

Update: Created a ticket to add this tool to the Main https://usegalaxy.org server: https://github.com/galaxyproject/usegalaxy-playbook/issues/220. I can’t predict how long that will take (could be few weeks, maybe less). Follow the ticket for updates, it will close out once done.

Meanwhile, try the EU server.

Thanks!

#5

Thank you both of you, amir and jennaj!
Because I’m new in Galaxy, I didn’t know there’s another Galaxy.
I’ll try it in Galaxy EU and thanks a lot for adding volcano plot to Galaxy Main.

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#6

Super, glad that helped.

There are even more ways/places to use Galaxy :earth_asia::earth_americas::earth_africa::cloud::computer:

If interested, please see: https://galaxyproject.org/use/

The general guideline is that you have one account per public Galaxy server. You’ll find different tools and analysis domain focuses across options, plus can customize your own when using a Cloud/Docker/Local version.