Please add the Xenopus laevis reference genome to Galaxy -- Indexing already planned, use a Custom Genome/Build for now

usegalaxy.org support
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I want to use Galaxy to analyze some RNA-seq data in the near future and would appreciate it if the Galaxy team could upload the Xenopus laevis reference genome! X. laevis is a model species so the genome should definitely be there! Everyone please upvote!

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I would like to second this request. I’m about to run RNA-seq and differential gene expression on Xenopus tissues and would like to use the Galaxy platform. Ideally, the Xenopus reference genome would be accessible in HISAT2 or some other alignment module.

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Hi @atschultz414 and @lauren.todd

This genome is already on the list of genomes that will be added to Galaxy. However, you shouldn’t wait – as that project will take some time to complete.

Instead, use a custom genome/build for now.

Thanks!

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Hi Jennifer,

Thank you for your feedback. The Galaxy EU server has X. laevis in their STAR alignment module, so I will be going through them for that step of the analysis. I do understand that this project will take a while, but when you say that, what exactly do you mean? Are you simply referring to how long the various calculations take at each step of the analysis through the server? I’m sorry, I’m a total novice, and your comment made me a little worried that I’m overlooking something :grin: As I understand it, Galaxy should be able to do everything, beginning with the initial read FASTQ file QC and alignment up through differential gene expression analysis, GO ontology and graphical visualization, correct? I only know basic programming, hence why I am doing all of this through Galaxy.

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The project’s goals are to:

  1. Add more genomes in general
  2. Fully index those for tools, filling in any current gaps
  3. Consolidate the existing genomes + indexes across usegalaxy.* servers and make them available to all from the centralized data repository. Currently, that data repository only contains genomes+indexes hosted at usegalaxy.org.

Using alternative public Galaxy servers such as usegalaxy.eu is a great choice if your genome is available there and indexed for the tools you plan to use. Larger genomes used as custom genomes/builds sometimes exceed computational resources. If a server has your genome of interest indexed, then that is less likely to be a problem.

Thanks!

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Jennifer,

Oh, I see what you were saying. Got it.

One more question. I have 24 FASTQ files (12 samples, each with 2 paired-end reads), which is 40.5 GB in total. To your knowledge, should the 250 GB account capacity be enough for me to complete all stages of analyses up through differential gene expression (using DESeq2) and graphical visualization?

Sorry for all the questions…

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@atschultz414 Ok – glad you understand now :slight_smile:

This might be possible. See this FAQ for help with data storage (quota) management strategies: Account quotas - Galaxy Community Hub