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Question: Retrieve canonical transcript for each gene via ensembldb R package
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gravatar for simon.boutry
29 days ago by
simon.boutry0 wrote:

I'm trying to retrieve the canonical transcript for each genes using ensembldb package. In the ensembl database there is a fiel canonical transcript in the gene table, which redirect you to the disered row in the transcript table. Therefore it is easy to obtain canonical transcript for each gene. But using ensembldb, I can't find that fiel "canonical transcript or any other way to retrieve the desired information (canonical transcript). Does someone know if there is such an "easy way" to obtain the answer ?

For the moment, based on the ensembldb I made a script implementing the procedure to compute the canonical transcript (as described on the ensembl website), it works, but is not as efficient as simply joining two tables.

Thanks in advance

annotation ensembldb • 127 views
ADD COMMENTlink modified 27 days ago by Johannes Rainer1.4k • written 29 days ago by simon.boutry0
Answer: Retrieve canonical transcript for each gene via ensembldb R package
1
gravatar for Johannes Rainer
27 days ago by
Johannes Rainer1.4k
Italy
Johannes Rainer1.4k wrote:

At present I am not including this information to the ensembldb databases. So there is no way to get the canonical transcript for a gene using ensembldb. Sorry for that.

ADD COMMENTlink written 27 days ago by Johannes Rainer1.4k
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