[BioC] biomaRt access for NCBIM37 build of mouse genome

[Christopher T Gregg]

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]]
>> 
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