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

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Fabrice Tourre ▴ 970

@fabrice-tourre-4394

Last seen 9.6 years ago

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="hsa piens_gene_ensembl") So I think is there a place to download the sqlite file directtly by http or ftp? Thanks.

TranscriptDb TranscriptDb • 1.1k views

ADD COMMENT • link updated 13.3 years ago by Michael Lawrence ★ 11k • written 13.3 years ago by Fabrice Tourre ▴ 970

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.4 years ago

United States

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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]]

ADD COMMENT • link 13.3 years ago Michael Lawrence ★ 11k

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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_gen e_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 >

ADD REPLY • link 13.3 years ago Marc Carlson ★ 7.2k

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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_ge ne_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 >> > > _______________________________________________ > 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 >

ADD REPLY • link 13.3 years ago Fabrice Tourre ▴ 970

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