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Question: Is there a place to download GenomicFeatures'
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gravatar for Wenzhang Wang
7.9 years ago by
Wenzhang Wang20 wrote:
Dear all, When I am trying to run the follwing codes , the R is dead with no response: either > txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene") or > txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="knownGene") And > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Chinese_People's Republic of China.936 LC_CTYPE=Chinese_People's Republic of China.936 LC_MONETARY=Chinese_People's Republic of China.936 [4] LC_NUMERIC=C LC_TIME=Chinese_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2 IRanges_1.8.7 loaded via a namespace (and not attached): [1] Biobase_2.10.0 biomaRt_2.6.0 Biostrings_2.18.2 BSgenome_1.18.2 DBI_0.2-5 RCurl_1.5-0.1 RSQLite_0.9-4 rtracklayer_1.10.6 [9] XML_3.2-0.2 Wenzhang Wang ************************************ State Key Lab of Genetic Engineering School of Lifescince Fudan University ************************************ Shanghai,China ************************************ > Message: 1 > Date: Wed, 15 Dec 2010 05:31:33 -0800 > From: Michael Lawrence <lawrence.michael at="" gene.com=""> > To: Fabrice Tourre <fabrice.ciup at="" gmail.com=""> > Cc: Bioconductor mailing list <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] Is there a place to download GenomicFeatures' > sqlite from ensembl. > Message-ID: > <aanlktinyb-cebch8whrag+mt6gxj-tho2qvpjgs_drmt at="" mail.gmail.com=""> > Content-Type: text/plain > > 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 >> >
ADD COMMENTlink modified 7.9 years ago by Steve Lianoglou12k • written 7.9 years ago by Wenzhang Wang20
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gravatar for Steve Lianoglou
7.9 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, On Thu, Dec 16, 2010 at 9:09 AM, Wenzhang Wang <052023069 at fudan.edu.cn> wrote: > Dear all, > > When I am trying to run the follwing codes , the R is dead with no response: > either > >> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene") > or >> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="knownGene") This is working for me -- perhaps you are having some connectivity problems? R> sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.1 IRanges_1.8.5 -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 7.9 years ago by Steve Lianoglou12k
Hi Wenzhang, I think Steve is probably right in that it sounds like you have a connection issue. In addition, once you get it downloaded, you will probably want to use saveFeatures() and loadFeatures() to preserve a local copy of your annotations. So you might want to look at that as well. Marc On 12/16/2010 07:53 AM, Steve Lianoglou wrote: > Hi, > > On Thu, Dec 16, 2010 at 9:09 AM, Wenzhang Wang <052023069 at fudan.edu.cn> wrote: > >> Dear all, >> >> When I am trying to run the follwing codes , the R is dead with no response: >> either >> >> >>> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene") >>> >> or >> >>> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="knownGene") >>> > This is working for me -- perhaps you are having some connectivity problems? > > R> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.1 IRanges_1.8.5 > >
ADD REPLYlink written 7.9 years ago by Marc Carlson7.2k
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