Please put Xenopus laevis genome on Galaxy

Question: Please put Xenopus laevis genome on Galaxy

7 months ago by

tamiredri • 10 wrote:

Hello,

Many labs using tools on Galaxy would like to see the Xenopus laevis genome as built-in genome for alignment. Xenopus tropicalis is there but not Xenopus laevis. The community uses both species and laevis is now available through NCBI.

https://www.ncbi.nlm.nih.gov/genome/81

It would be great if you could import these data ASAP, as the research is fast and furious right now in both species. The Xenopus community would greatly appreciate it.

Thanks, Tamir

laevis xenopus rna-seq • 276 views

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modified 7 months ago by Bjoern Gruening ♦ 5.1k • written 7 months ago by tamiredri • 10

7 months ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Xenopus laevis should be available at https://usegalaxy.eu.

ADD COMMENT • link written 7 months ago by Bjoern Gruening ♦ 5.1k

7 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

We are updating our protocols for creating new indexes over the next few weeks, so adding new Reference genomes immediately is likely not possible (we are still discussing the details based on your original email request). Once the larger strategy for new data additions is settled, we will add both genomes as natively indexed builds. Reference annotation associated with the builds will still need to be uploaded per-user, or you can create a shared/published history with the data to grant access to others.

Meanwhile, both the genomes and associated reference annotation can be uploaded to Galaxy and placed in a history that can be shared/published. You'll be using the Custom genome/build functions with tools. It is very important that the data is formatted/labeled correctly or tool errors can result. Please see the help here for details:

Preparing and using a Custom Reference Genome or Build https://galaxyproject.org/learn/custom-genomes/
Mismatched Chromosome identifiers (and how to avoid them) https://galaxyproject.org/support/chrom-identifiers/
Sharing and Publishing your work https://galaxyproject.org/learn/share/
Support FAQs: https://galaxyproject.org/support/
Galaxy Tutorials: https://galaxyproject.org/learn/

Ticket: https://github.com/galaxyproject/galaxy/issues/1470#issuecomment-385775730

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson ♦ 25k

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