[BioC] Using Biomart other than Ensembl

[James W. MacDonald]

Hi Daniela,

On 2/26/2014 2:29 PM, Daniela Moré [guest] wrote:
> Hi guys,
> I'm new on R and Bioconductor packages so my question can sounds a little basics but I really could not figure out how to use a database from NCBI in BiomaRt.
> I'm working on RNA-Seq reads to perform DE analysis and I'm interested in Bos taurus database from NCBI version UMD3.1.

I think you will need to give more information here. What exactly are 
you trying to do? Have you already done the DE analysis, and now are 
simply trying to annotate the results? If so, what type of 
gene/transcript IDs do you have?

Best,

Jim


>
> So my question is: how to choose the bovine UMD3.1 from NCBI in BiomaRt? Or the best way to solve this would be to perform the aligment using the ensembl version?
>
> Just to make me clear I can't find any NCBI databases when I type:
>
>> library("biomaRt")
>> listMarts()
>   If I take a look at “ensembl” [ensembl=useMart("ensembl")] so I can see the btaurus_gene_ensembl dataset. However, as I aligned my reads against a NCBI version when I tried count the reads, it did not work ('cause they have different identifiers I guess). The manual shows a short example using a wormDb but it did not help so much.
>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] DESeq2_1.2.10           RcppArmadillo_0.4.000.2 Rcpp_0.11.0             Rsamtools_1.14.3        Biostrings_2.30.1       GenomicRanges_1.14.4
> [7] XVector_0.2.0           IRanges_1.20.6          BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.24.0   BSgenome_1.30.0        Biobase_2.22.0         DBI_0.2-7              GenomicFeatures_1.14.2 RColorBrewer_1.0-5
>   [7] RCurl_1.95-4.1         RSQLite_0.11.4         XML_3.98-1.1           annotate_1.40.0        biomaRt_2.18.0         bitops_1.0-6
> [13] genefilter_1.44.0      grid_3.0.2             lattice_0.20-24        locfit_1.5-9.1         rtracklayer_1.22.3     splines_3.0.2
> [19] stats4_3.0.2           survival_2.37-7        tools_3.0.2            xtable_1.7-1           zlibbioc_1.8.0
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099