[BioC] biomaRt access for NCBIM37 build of mouse genome

[Hans-Rudolf Hotz]

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]]
>
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