[BioMart Users] Variation Biomart filters and source databases query

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[BioMart Users] Variation Biomart filters and source databases query

Buxton Chris (NORTH BRISTOL NHS TRUST)

Hi,

 

I am have a little difficulty adding the filter criteria to the variation dataset in Biomart to get variation records for a set of genomic coordinates.

Under the “Multiple Chromosomal Regions (Chr:Start:End:Strand)” part, could someone please clarify the format of the filter as I cant get it to find any SNPs

 

 

 

Also, what is the difference between  Homo sapiens Structural variation and Homo sapiens variation.

My assumption is that variation is single nucleotide polymorphisms, and structural variation is indels? 

Any clarification would be helpful

 

 

Thanks,

 

Chris

 

 


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Re: [BioMart Users] Variation Biomart filters and source databases query

Rhoda Kinsella
Hi Chris,
The strand needs to be set to either 1 or -1. I hope that helps.
Regards
Rhoda


On 15 Dec 2011, at 15:48, Buxton Chris (NORTH BRISTOL NHS TRUST) wrote:

Hi,
 
I am have a little difficulty adding the filter criteria to the variation dataset in Biomart to get variation records for a set of genomic coordinates.
Under the “Multiple Chromosomal Regions (Chr:Start:End:Strand)” part, could someone please clarify the format of the filter as I cant get it to find any SNPs
 
<image003.jpg>
 
 
Also, what is the difference between  Homo sapiens Structural variation and Homo sapiens variation.
My assumption is that variation is single nucleotide polymorphisms, and structural variation is indels? 
Any clarification would be helpful
<image004.jpg>
 
 
Thanks,
 
Chris
 
 

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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus, 
Hinxton
Cambridge CB10 1SD,
UK.


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Re: [BioMart Users] Variation Biomart filters and source databases query

Arek Kasprzyk
In reply to this post by Buxton Chris (NORTH BRISTOL NHS TRUST)
Hi Chris,
I just checked and it seems that there is a problem with this filter in the 0.8 server. You need to bear with us until we fix this problem. As a backup you can still use this filter in the old 0.7 server:

http://www.biomart.org/biomart/martview/

the filter input format is:

1:100:10000000:1

a



On Thu, Dec 15, 2011 at 10:48 AM, Buxton Chris (NORTH BRISTOL NHS TRUST) <[hidden email]> wrote:

Hi,

 

I am have a little difficulty adding the filter criteria to the variation dataset in Biomart to get variation records for a set of genomic coordinates.

Under the “Multiple Chromosomal Regions (Chr:Start:End:Strand)” part, could someone please clarify the format of the filter as I cant get it to find any SNPs

 

 

 

Also, what is the difference between  Homo sapiens Structural variation and Homo sapiens variation.

My assumption is that variation is single nucleotide polymorphisms, and structural variation is indels? 

Any clarification would be helpful

 

 

Thanks,

 

Chris

 

 


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