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

[Fabrice Tourre]

Thanks.

I changed a computer. It works well.

On Wed, Dec 15, 2010 at 7:47 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> 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.
>>
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