Question: Convert Gene IDs into ENTREZ or ENSEMBL format (honey bee / apis mellifera)
0
gravatar for LRStar
2.3 years ago by
LRStar190
United States
LRStar190 wrote:

Hello,

I am trying to use the getGeneLengthAndGCContent() function from the EDASeq R package to obtain gene lengths and GC content for each gene in a honeybee (apis mellifera) dataset. An example subset of these genes are as follows:

"GB40001" "GB40002" "GB40003" "GB40004" "GB40005" "GB40006"

Upon running the command on an example gene as follows and using the code for apis mellifera ("ame"):

getGeneLengthAndGCContent("GB40001", org="ame")

I receive the error:

Error in getGeneLengthAndGCContent("GB40001", org = "ame", mode = "org.db") : Only ENTREZ or ENSEMBL gene IDs are supported.

How can I convert my list of genes (in format of GB40001) into a list of ENTREZ or ENSEMBL gene IDs?

Thank you for any support on accomplishing this step.

rna-seq entrez ensembl • 1.1k views
ADD COMMENTlink modified 2.3 years ago by Emily_Ensembl20k • written 2.3 years ago by LRStar190
1
gravatar for Denise - Open Targets
2.3 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.1k wrote:

It seems IDs such as GB40001 are THE Gene IDs used in Ensembl Metazoa.

ADD COMMENTlink written 2.3 years ago by Denise - Open Targets5.1k

Thanks, Denise. Just checking, but how should I interpret this Error then if it seems I am providing the correct information?

ADD REPLYlink written 2.0 years ago by LRStar190
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