[BioC] biomaRt get exon intron structure of a transcrit
shidaxia at yahoo.com
Thu Nov 13 01:59:28 CET 2008
That was very helpful. Thank you very much!
From: "steffen at stat.Berkeley.EDU" <steffen at stat.Berkeley.EDU>
Cc: James W. MacDonald <jmacdon at med.umich.edu>; johannes.rainer at tugraz.at; bioconductor at stat.math.ethz.ch
Sent: Tuesday, November 11, 2008 10:11:46 AM
Subject: Re: [BioC] biomaRt get exon intron structure of a transcrit
There isn't a difference between sequence_exon_chrom_start and
exon_chrom_start in terms of the output. These attributes are both there
as they correspond to different 'attribute pages' which is not directly
relevant for the biomaRt API but is for the BioMart web interface. BioMart
puts limits on the number of attributes you can retrieve from different
pages/categories, this is actually zero and you have to stick within one
page. biomaRt is a little more relaxed on this but it is still
recommended to stick to querying attributes within one page/category in
So, I would suggest using exon_chrom_start if you don't retrieve any
sequence data and use sequence_exon_chrom_start if you do retrieve
sequences in the same biomaRt query.
You can see to which page/category attributes belong to by:
> mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
> attrib = listAttributes(mart, showGroups=TRUE)
name description group category
1 affy_hc_g110 AFFY HC G110 EXTERNAL: Features
2 affy_hg_focus AFFY HG FOCUS EXTERNAL: Features
3 affy_hg_u133a AFFY HG U133A EXTERNAL: Features
4 affy_hg_u133a_2 AFFY HG U133A_2 EXTERNAL: Features
5 affy_hg_u133b AFFY HG U133B EXTERNAL: Features
6 affy_hg_u133_plus_2 AFFY HG U133-PLUS-2 EXTERNAL: Features
> 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.
> ----- Original Message ----
> From: James W. MacDonald <jmacdon at med.umich.edu>
> 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?
>> "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
> 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.
>> i just wanted to know if it is possible to get the exon intron structure
>> a transcript from biomaRt (i.e. exon 1: start=..., stop=..., exon 2:...)
>> bests, jo
> -- James W. MacDonald, M.S.
> Hildebrandt Lab
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> 1150 W. Medical Center Drive
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