Question: How to convert gencode ID into ENSEMBL ID
gravatar for mirjam.podgorica
8 days ago by
mirjam.podgorica0 wrote:

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

rna-seq galaxy • 53 views
ADD COMMENTlink modified 7 days ago • written 8 days ago by mirjam.podgorica0
gravatar for Jennifer Hillman Jackson
7 days ago by
United States
Jennifer Hillman Jackson25k wrote:


The identifiers are probably already in Ensembl format:

There is a known issue with the Uniprot ID mapping tool at Galaxy Main We will be updating it plus adding another annotation ID conversion tool near term. Details:

For now, please try using the Galaxy Europe server for this functionality instead (tool options: Uniprot ID mapping or AnnotateMyIDs):

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 days ago by Jennifer Hillman Jackson25k
gravatar for mirjam.podgorica
7 days ago by
mirjam.podgorica0 wrote:

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

ADD COMMENTlink written 7 days ago by mirjam.podgorica0

Try using identifiers without the version included. For example, query with this ENSG00000114268 instead of this ENSG00000114268.11.

ADD REPLYlink written 5 days ago by Jennifer Hillman Jackson25k
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