Sorry, what you mean by start-end for SNPs? That does seem to be a tedious task. I would suggest contacting Ensembl Helpdesk to see if they can recommend another way of doing this, but from what it looks like, this may have to be done in two steps.
Please don’t hesitate to ask any questions. I'd be glad to try and help. Elena From: Matthias Macé <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Mon, 14 Mar 2011 14:38:04 -0400 To: Microsoft Office User <[email protected]<mailto:[email protected]>> Cc: Arek Kasprzyk <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]> >> \"[email protected]<mailto:[email protected]>\"" <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] Biomart xml query Elena, OK, that's what I thought : it seems impossible to directly retrieve the result. So why is there the 'start-end' SNP option ? It seems useless, isn't it ? I hoped to perform this task in one "shot" since I plan to do this on more than 30 000 queries. I hope I do not bother you with my (stupid) questions... Many thanks, Matthias Al 14/03/2011 19:19, En/na Elena Rivkin ha escrit: Matthias, I used your SNPs in 'Ensembl variation' and I got the following coordinates (see attached. rs12885778 (chr 14) 20404091 rs4399482 (chr 14) 20137587 XML query: <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE Query> <Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" > <Dataset name = "hsapiens_snp" interface = "default" > <Filter name = "refsnp" value = "rs4399482,rs12885778"/> <Attribute name = "refsnp_id" /> <Attribute name = "chr_name" /> <Attribute name = "chrom_start" /> </Dataset> </Query> Entering these bp into gene search I got 10 genes (see attached). XML query: <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE Query> <Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" > <Dataset name = "hsapiens_gene_ensembl" interface = "default" > <Filter name = "chromosome_name" value = "14"/> <Filter name = "end" value = "20404091"/> <Filter name = "start" value = "20137587"/> <Attribute name = "ensembl_gene_id" /> <Attribute name = "ensembl_transcript_id" /> </Dataset> </Query> Elena On 11-03-14 2:08 PM, "Matthías Macé" <[email protected]><mailto:[email protected]> wrote: Elena, FIrst, thank you for your valuable help. I tried your method (using rs4399482 <-> rs12885778). By querying UCSC, they return "OR11H2,OR4K1,OR4K2,OR4K5,OR4M1,OR4N2,OR4Q3". However, when I try with Biomart, I get an empty field (with either ENsembl ID or HGNC). I queried dbSNP and for the first SNP, it told me that it was an Illumina SNP. I replaced with the corresponding dbSNP ID once more, it failed. Any idea ? Best regards, Matthias Al 14/03/2011 17:03, En/na Elena Rivkin ha escrit: Matthias, Just to add to Arek's suggestion you can also try using the 'Marker' filters in the REGION section. If this does not work, SNPs can be converted to their genomic coordinates (this can be done using Ensembl variation datasets), and then these coordinates can be used to identify the genes. Elena From: Arek Kasprzyk <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Date: Mon, 14 Mar 2011 11:45:52 -0400 To: "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>>, "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Subject: Re: [BioMart Users] Biomart xml query Ok, I got it. Perhaps multiple genomic region filter could the the trick. Input coordinate segments there and output the genes Try Ensembl 61, Home sapiens genes, 'REGION' section, "multpile chromosomal regions". See if this helps a Arek Kasprzyk Director, Bioinformatics Operations and Principal Investigator Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8559 Toll-free: 1-866-678-6427 www.oicr.on.ca<http://www.oicr.on.ca> Administrative Assistant: [email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. From: Matthias Macé <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>>, "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Date: Mon, 14 Mar 2011 11:40:10 -0400 To: Arek Kasprzyk <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Subject: Re: [BioMart Users] Biomart xml query Hi Arek, No, I give the following input : rsID_1 rs_ID_2 and i wish to retrieve a list of genes at least overlapping with the segment "rs_ID_1<-->rs_ID_2". query: rs_ID_1---------------------------rs_ID_2 <-----------gene_1-------------> <-------gene_2---------> <-----------gene_3-------------> It would return : gene_1, gene_2, gene_3 Thanks, Matthias Al 14/03/2011 16:30, En/na Arek Kasprzyk ha escrit: Hi MM, Are you asking for the SNP/gene consequences such as 'non_synonymous', 'intronic' etc? a Arek Kasprzyk Director, Bioinformatics Operations and Principal Investigator Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8559 Toll-free: 1-866-678-6427 www.oicr.on.ca<http://www.oicr.on.ca><http://www.oicr.on.ca><http://www.oicr.on.ca> Administrative Assistant: [email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. From: Matthias Macé <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:matthias. [email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:matthias. [email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:matthias. [email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>>, "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:matthias. [email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:matthias. [email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Date: Mon, 14 Mar 2011 11:22:30 -0400 To: Arek Kasprzyk <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:arek.ka [email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Subject: Re: [BioMart Users] Biomart xml query Dear Arek, Many thanks for your quick answer ! However, I already did what you tlod me on a previous query, but now, my problem is that I cannot find the mapping I told you on the web-based interface (i.e. snp segment >> overlapping genes). I can only retrieve annotation for every snp. Isn't there any way to perform "segment-query" ? Cheers, MM Al 14/03/2011 15:57, En/na Arek Kasprzyk ha escrit: Director, Bioinformatics Operations and Principal Investigator -- "Only two things are infinite, the universe and human stupidity, and I'm not sure about the former." -Albert Einstein Dr Matthias Macé, DVM, PhD INSERM U1043 C.H.U. Purpan - BP 3028 31024 TOULOUSE CEDEX 3 tel: (33) 562 74 45 09 mobile: (33) 608 881481 http://www.u563.toulouse.inserm.fr/ -- "Only two things are infinite, the universe and human stupidity, and I'm not sure about the former." -Albert Einstein Dr Matthias Macé, DVM, PhD INSERM U1043 C.H.U. Purpan - BP 3028 31024 TOULOUSE CEDEX 3 tel: (33) 562 74 45 09 mobile: (33) 608 881481 http://www.u563.toulouse.inserm.fr/ -- "Only two things are infinite, the universe and human stupidity, and I'm not sure about the former." -Albert Einstein -- "[...] si un jour nos villes et nos campagnes sont enfin libérées de cette détestable présence exotique [les immigrés], eh bien, ce jour-là,c¹est simplement que ce seront les chers enfants de Lille, de Nantes, de Sheffield ou de Birmingham qui prendront leur baluchon, feront leurs adieux et partiront vivre, travailler, aimer et mourir ailleurs." [http://bloginlondon.wordpress.com/2010/01/29/les-anglais-decouvrent-les-c harmes-du-lepenisme/] -- "Only two things are infinite, the universe and human stupidity, and I'm not sure about the former." -Albert Einstein Dr Matthias Macé, DVM, PhD INSERM U1043 C.H.U. Purpan - BP 3028 31024 TOULOUSE CEDEX 3 tel: (33) 562 74 45 09 mobile: (33) 608 881481 http://www.u563.toulouse.inserm.fr/
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