[BioC] biomaRt get exon intron structure of a transcrit

[Shi, Tao]

Hi Jim,

Thank you very much!  It works.  

I didn't look further down in   listAttributes(mart), so I missed those.

Do you know the difference between "sequence_exon_chrom_start" vs. "exon_chrom_start"?

...Tao





----- Original Message ----
From: James W. MacDonald <jmacdon at med.umich.edu>
To: "Shi, Tao" <shidaxia at yahoo.com>
Cc: bioconductor at stat.math.ethz.ch; johannes.rainer at tugraz.at
Sent: Friday, November 7, 2008 11:46:30 AM
Subject: Re: [BioC] biomaRt get exon intron structure of a transcrit

Hi Tao,

Does this do what you want?

> getBM(c("ensembl_gene_id", "sequence_exon_chrom_start","sequence_exon_chrom_end"), "ensembl_gene_id", "ENSG00000204580", mart)
   ensembl_gene_id exon_chrom_start exon_chrom_end
1  ENSG00000204580         30960306       30960466
2  ENSG00000204580         30961381       30961436
3  ENSG00000204580         30964444       30964570
4  ENSG00000204580         30964664       30964766
5  ENSG00000204580         30964958       30965186



Best,

Jim

Shi, Tao wrote:
> Hi list,
> 
> I have the same question like this old post, but don't see any answers.  Wonder whether we have any answers now.
> 
> Thanks,
> 
> ...Tao
> 
> 
> 
> ======================================================================================
> https://stat.ethz.ch/pipermail/bioconductor/attachments/20070717/ef7264e5/attachment.pl
> 
> hi,
> i just wanted to know if it is possible to get the exon intron structure of
> a transcript from biomaRt (i.e. exon 1: start=..., stop=..., exon 2:...)
> bests, jo
> 

-- James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-5646
734-936-8662