biomaRt get exon intron structure of a transcrit
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
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/ef726 4e5/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 -- Johannes Rainer, Msc Tyrolean Cancer Research Institute Innrain 66, 6020 Innsbruck, Austria Tel.: +43 512 570485 33 Email: johannes.rainer at tcri.at johannes.rainer at tugraz.at [[alternative HTML version deleted]]
Cancer biomaRt Cancer biomaRt • 1.2k views
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
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@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/ef7 264e5/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
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Hi Tao, 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 one query. 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: > library(biomaRt) > mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") > attrib = listAttributes(mart, showGroups=TRUE) > head(attrib) 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 Cheers, Steffen > 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/ef 7264e5/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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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@james-w-macdonald-5106
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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/ef7 264e5/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
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
Hi Steffen, That was very helpful. Thank you very much! ...Tao ________________________________ From: "steffen@stat.Berkeley.EDU" <steffen@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 Hi Tao, 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 one query. 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: > library(biomaRt) > mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") > attrib = listAttributes(mart, showGroups=TRUE) > head(attrib) 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 Cheers, Steffen > 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=""> > 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/ef 7264e5/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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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