Hi, I have gene Id derived from gencode and I am trying to convert into gene names, but i think I need to convert to ensembl before because the tool is not recognizing them. I am using UNIprot in galaxy. Is there a suggestion how to do that and is there any other tools i can use to get the gene names from ID in galaxy?
Thank you in advance
Best, Mirjam
Hello,
The identifiers are probably already in Ensembl format: https://www.gencodegenes.org/pages/faq.html
There is a known issue with the Uniprot ID mapping tool at Galaxy Main https://usegalaxy.org. We will be updating it plus adding another annotation ID conversion tool near term. Details: https://github.com/search?q=org%3Agalaxyproject+uniprot&type=Issues
For now, please try using the Galaxy Europe server for this functionality instead (tool options: Uniprot ID mapping or AnnotateMyIDs): https://usegalaxy.eu
Thanks! Jen, Galaxy team
Hi thank you for the answer I tried annotate my id but it doesnt recognize the geen id and it give em an error Fatal error: Exit code 1 () Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments. Calls: select ... select -> .select -> testSelectArg
My gene id are ENSG00000114268.11 so im not sure whether the point is the problem and makes it unrecognizable
Best, Mirjam
