I am trying to use the getGeneLengthAndGCContent function from the EDASeq library to retrieve gene lengths for c. elegans. I retrieved Ensemble gene ids from Biomart for c.elegans and I'm using those as input to getGeneLengthAndGCContent (I picked "ensemble_gene_id" from the filters of the worm annotation Mart). Here's an example of how I'm trying to use the function:

getGeneLengthAndGCContent("WBGene00001042", org, mode=c("biomart", "org.db"))

When I try to run this, I get

Error in getGeneLengthAndGCContent("WBGene00001042", org, mode = c("biomart",  : 
  Only ENTREZ or ENSEMBL gene IDs are supported.
  • $\begingroup$ @ATpoint oh that's weird why does BioMart list it as such? $\endgroup$ Jun 18 '20 at 14:51
  • $\begingroup$ @ATpoint also when I look at Ensembl I don't find any other identifier for a gene of c elegans (here's an example uswest.ensembl.org/Caenorhabditis_elegans/Gene/…). Could you guide me as to where to find those other ids? $\endgroup$ Jun 18 '20 at 14:52
  • $\begingroup$ Never mind, I was wrong. $\endgroup$
    – ATpoint
    Jun 18 '20 at 17:44
  • $\begingroup$ @ATpoint so WBGene00001042 is indeed the Ensembl id? $\endgroup$ Jun 18 '20 at 22:16

I found my answer here. It uses getGeneLengthAndGCContent but changes a small part of the function.


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