Hello, I am planning to perform mapping using the tool RNA STAR with the C. elegans reference genome WBcel235/ce11 which is currently missing. Is it possible to add this? Thank you!
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Welcome, @ClaireYShen
I see the UCSC version of the ce11 reference genome at the UseGalaxy.eu server. Does this help?
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You can get the reference annotation file for this genome from UCSC. Copy the link from their Downloads area into the Upload tool, use all default settings, and that will load as an uncompressed GTF file into your history.
Instructions → FAQ: Working with GFF GFT GTF2 GFF3 reference annotation
- Starting from here → UCSC Genome Browser Downloads
- Find the ce11 files here → UCSC Genome Browser Downloads
- Then navigate into this data directory → Index of /goldenPath/ce11/bigZips/genes
You can explore what those different annotation tracks represent in the UCSC Genome Browser itself. → UCSC Genome Browser Gateway
If you want to pull in annotation from another source, the instructions can differ a bit but this is usually possible. Please let us know if you need help with that, and you can review prior Q&A about troubleshooting reference data issues in topics with this tag but also others → reference-annotation
And, for anyone else reading, if you ever need to work with a reference genome that is not hosted at the server where you are working, and there isn’t an alternative or you just don’t want to switch servers, you can always use the Custom Reference Genome function. Any genome can be used this way, and you’ll still be loading reference annotation the same as above. See → FAQ: How to use Custom Reference Genomes? with prior Q&A discussed across topics, but those will usually have this tag → custom-genome or custom-build (the “build” is a custom database key if needed)
Please let us know if this helps or if you have more questions! 