On Wed, Dec 15, 2010 at 2:03 AM, Fabrice Tourre <fabrice.ciup@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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