[BioC] Is there a place to download GenomicFeatures' sqlite from ensembl.

[Marc Carlson]

Hi Fabrice,

This is an odd report because that same line of code works flawlessly
for me and produces a local DB in mere minutes.  Are you able to access
ensemble using biomaRt from your computer?  Because that is how
makeTranscriptDbFromBiomart() will get it's data.


  Marc



On 12/15/2010 05:31 AM, Michael Lawrence wrote:
> On Wed, Dec 15, 2010 at 2:03 AM, Fabrice Tourre <fabrice.ciup at gmail.com>wrote:
>
>   
>> Dear all,
>> I am trying to make TranscriptDb Object. First I used
>> makeTranscriptDbFromUCSC, it is no problem. The command is this:
>> library("GenomicFeatures")
>> hg19KG <- makeTranscriptDbFromUCSC(genome = "hg19", tablename =
>> "knownGene")
>>
>> But I also want to look the anotation from ensembl, some isoform
>> defined different in ucsc and ensembl. I run this comand, it took two
>> days and not finished.
>> library("GenomicFeatures")
>> hgensembl<-
>> makeTranscriptDbFromBiomart(biomart="ensembl",dataset="hsapiens_gene_ensembl")
>>
>> So I think is there a place to download the sqlite file directtly by
>> http or ftp?
>>
>>
>>     
> No, but that sounds like a bug. I would mention though that UCSC has the
> Ensembl gene predictions, under the "ensGene" table.
>
> Thanks.
>   
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>     
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>