[BioC] Is there a place to download GenomicFeatures' sqlite from ensembl.
mcarlson at fhcrc.org
Wed Dec 15 19:47:50 CET 2010
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.
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:
>> hg19KG <- makeTranscriptDbFromUCSC(genome = "hg19", tablename =
>> 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.
>> 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.
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