biomaRt access for NCBIM37 build of mouse genome

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Christopher T Gregg ▴ 210

@christopher-t-gregg-4973

Last seen 9.6 years ago

Hello, I am using biomaRt. I want to retrieve transcript start and stop info based on the NCBIM37 (mm9) build using getBM. I can't find this annotation in listMarts(archive =T). Is anyone aware of a simple solution? Thank you. best wishes, Chris > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_3.0.8 limma_3.14.1 rtracklayer_1.18.0 biomaRt_2.14.0 GenomicRanges_1.10.5 IRanges_1.16.4 BiocGenerics_0.4.0 [8] Gviz_1.2.0 loaded via a namespace (and not attached): [1] annotate_1.36.0 AnnotationDbi_1.20.2 Biobase_2.18.0 Biostrings_2.26.2 biovizBase_1.6.0 bitops_1.0-4.2 [7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-0 DBI_0.2-5 DESeq_1.10.1 dichromat_1.2-4 [13] genefilter_1.40.0 geneplotter_1.36.0 GenomicFeatures_1.10.0 Hmisc_3.10-1 labeling_0.1 lattice_0.20-10 [19] munsell_0.4 parallel_2.15.2 plyr_1.7.1 RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.1 [25] RSQLite_0.11.2 scales_0.2.2 splines_2.15.2 stats4_2.15.2 stringr_0.6.1 survival_2.36-14 [31] tools_2.15.2 XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 [[alternative HTML version deleted]]

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ADD COMMENT • link updated 11.1 years ago by Hotz, Hans-Rudolf ▴ 400 • written 11.1 years ago by Christopher T Gregg ▴ 210

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Hotz, Hans-Rudolf ▴ 400

@hotz-hans-rudolf-3951

Last seen 3.5 years ago

Switzerland

Hi Chris use one of the archives. 'ensembl67' ("may2012.archive.ensembl.org") was the last ensembl release containing NCBIM37 (if I remember correctly). So you can try: > library(biomaRt) > ensembl67=useMart(host='may2012.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL') > listDatasets(ensembl67)[grep("Mus", listDatasets(ensembl67)$description),] dataset description version 48 mmusculus_gene_ensembl Mus musculus genes (NCBIM37) NCBIM37 > Regards, Hans-Rudolf On 03/13/2013 04:35 AM, chris_utah wrote: > Hello, > > I am using biomaRt. I want to retrieve transcript start and stop info based on the NCBIM37 (mm9) build using getBM. I can't find this annotation in listMarts(archive =T). Is anyone aware of a simple solution? > > Thank you. > > best wishes, > Chris > > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] edgeR_3.0.8 limma_3.14.1 rtracklayer_1.18.0 biomaRt_2.14.0 GenomicRanges_1.10.5 IRanges_1.16.4 BiocGenerics_0.4.0 > [8] Gviz_1.2.0 > > loaded via a namespace (and not attached): > [1] annotate_1.36.0 AnnotationDbi_1.20.2 Biobase_2.18.0 Biostrings_2.26.2 biovizBase_1.6.0 bitops_1.0-4.2 > [7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-0 DBI_0.2-5 DESeq_1.10.1 dichromat_1.2-4 > [13] genefilter_1.40.0 geneplotter_1.36.0 GenomicFeatures_1.10.0 Hmisc_3.10-1 labeling_0.1 lattice_0.20-10 > [19] munsell_0.4 parallel_2.15.2 plyr_1.7.1 RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.1 > [25] RSQLite_0.11.2 scales_0.2.2 splines_2.15.2 stats4_2.15.2 stringr_0.6.1 survival_2.36-14 > [31] tools_2.15.2 XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 > > > > > [[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 COMMENT • link 11.1 years ago Hotz, Hans-Rudolf ▴ 400

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Thank you, Hans-Rudolf. I greatly appreciate this tip. best wishes, Chris On Mar 13, 2013, at 2:40 AM, Hans-Rudolf Hotz <hrh at="" fmi.ch=""> wrote: > Hi Chris > > use one of the archives. 'ensembl67' ("may2012.archive.ensembl.org") was the last ensembl release containing NCBIM37 (if I remember correctly). > > So you can try: > > > library(biomaRt) > > > ensembl67=useMart(host='may2012.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL') > > > listDatasets(ensembl67)[grep("Mus", listDatasets(ensembl67)$description),] > dataset description version > 48 mmusculus_gene_ensembl Mus musculus genes (NCBIM37) NCBIM37 > > > > > > Regards, Hans-Rudolf > > > > On 03/13/2013 04:35 AM, chris_utah wrote: >> Hello, >> >> I am using biomaRt. I want to retrieve transcript start and stop info based on the NCBIM37 (mm9) build using getBM. I can't find this annotation in listMarts(archive =T). Is anyone aware of a simple solution? >> >> Thank you. >> >> best wishes, >> Chris >> >> >>> sessionInfo() >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] edgeR_3.0.8 limma_3.14.1 rtracklayer_1.18.0 biomaRt_2.14.0 GenomicRanges_1.10.5 IRanges_1.16.4 BiocGenerics_0.4.0 >> [8] Gviz_1.2.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.36.0 AnnotationDbi_1.20.2 Biobase_2.18.0 Biostrings_2.26.2 biovizBase_1.6.0 bitops_1.0-4.2 >> [7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-0 DBI_0.2-5 DESeq_1.10.1 dichromat_1.2-4 >> [13] genefilter_1.40.0 geneplotter_1.36.0 GenomicFeatures_1.10.0 Hmisc_3.10-1 labeling_0.1 lattice_0.20-10 >> [19] munsell_0.4 parallel_2.15.2 plyr_1.7.1 RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.1 >> [25] RSQLite_0.11.2 scales_0.2.2 splines_2.15.2 stats4_2.15.2 stringr_0.6.1 survival_2.36-14 >> [31] tools_2.15.2 XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 >> >> >> >> >> [[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 >>

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