[Genome] Questions on update, dumps and SNPs of hg18 data subsets ---knownGene*, refGene* and SNP

[Fangcheng Gong]

Hi Heather,

Thank you very much for your effort.  Yes, you're right, I'm looking at 
single base substitutions. The coordinates should be relative to the start 
of each specific transcript instead of gene as some genes have multiple 
transcripts, and the coordinates of the same SNPs on individual 
transcripts might be different due to the splicing. 

Regards,
Fangcheng




Heather Trumbower <heather at soe.ucsc.edu> 
02/14/2007 12:55 PM

To
Fangcheng Gong <Fangcheng.Gong at sial.com>
cc
genome at soe.ucsc.edu
Subject
Re: [Genome] Questions on update, dumps and SNPs of hg18 data subsets 
---knownGene*, refGene* and SNP






Thanks.

What do you mean by type of SNP?  Functional assignment?
For example: coding-synon, coding-nonsynon, untranslated, intron.

I am assuming you are refering to single base substitutions only.

Let's look at a specific example.

chr22:29,807,250-29,807,500 in hg18 has 2 SNPs in the initial 
part of the 5' UTR of SMTN.   They are single base substitutions 
at rs9609221 at position 29807313 and rs11089487 at position 29807360.

Do you want the SNP specified in absolute coordinates, or relative to the 
start of the gene annotation?

Heather



On Wed, 14 Feb 2007, Fangcheng Gong wrote:

> Hi Heather,
>
> Transcript SNP data is cSNP.  I consider the SNPs, mapped onto the 
RefSeq
> or other type of transcripts, as transcript SNP.  The transcript SNP
> should consists of the transcript accession, SNP coordinates on the
> transcript, and type of SNPs.
>
> Thanks,
> Fangcheng
>
>
>
>
> Heather Trumbower <heather at soe.ucsc.edu>
> 02/14/2007 12:00 PM
>
> To
> Fangcheng Gong <Fangcheng.Gong at sial.com>
> cc
> genome at soe.ucsc.edu
> Subject
> Re: [Genome] Questions on update, dumps and SNPs of hg18 data subsets
> ---knownGene*, refGene* and SNP
>
>
>
>
>
>
> Fangcheng:
>
> Could you clarify what you mean by transcript SNP data?
>
> Thanks.
>
> Heather Trumbower
> UCSC Genome Bioinformatics Group
>
>
> On Wed, 14 Feb 2007, Fangcheng Gong wrote:
>
>> Dear UCSC colleagues,
>>
>> 1) The following data files haven't updated for long time.  Could you
>> update them at your earliest convenience?
>>
>> Directory: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/
>>
>> knownGene.txt.gz        (the last update 04/13/2006)
>> knownGeneMrna.txt.gz    (the last update 04/13/2006)
>>
>> 2) Could you upload the dumps for the following files at the same
>> directory?
>>
>> refGeneMrna.sql
>> refGeneMrna.txt.gz
>>
>> 3) Do you have transcript SNP data for knownGene and refGene?  If yes,
> is
>> it possible to upload their dump at this FTP site?
>>
>>
>> Thank you very much for your time and effort.  I'm eager to hear your
>> reply.
>>
>> Regards
>> Fangcheng Gong
>>
>> _______________________________________
>> Fangcheng Gong, Ph.D.
>> Principal R&D Scientist, Bioinformatics
>>
>> Sigma-Aldrich Corporation
>> 2909 Laclede Ave.
>> St. Louis, MO 63103
>>
>> Phone:  314-289-8496 x 4464
>>        877-472-2192 x 4464
>> Fax:    314-286-7645
>> Email:  Fangcheng.Gong at sial.com
>> _______________________________________
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>
>
>