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

[Fangcheng Gong]

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
>