Hi Mary,
I have another question need your help. I have 5 version snp downloaded.
However, I found that some SNPs have quite different locus even in the same
file (for example the one rs648663 I attached below). And it looks like all
the other information is the same. Would you please let me know why it's in
such way? Thanks a lot.
Ying
===============================
snp128_chr22:716 chr22 17187821 17187822 rs648663
0 + A A A/C genomic single by-2hit-2allele 0
0 intron
exact 1
snp129_chr22:716 chr22 17187821 17187822 rs648663
0 + A A A/C genomic single by-2hit-2allele 0
0 intron
exact 2
snp129_chr22:737 chr22 19939068 19939069 rs648663
0 + A A A/C genomic single by-2hit-2allele 0
0 intron
exact 2
snp130_chr22:728 chr22 18807821 18807822 rs648663
0 + A A A/C genomic single by-2hit-2allele 0
0 unknow
n exact 2
snp130_chr22:749 chr22 21609068 21609069 rs648663
0 + A A A/C genomic single by-2hit-2allele 0
0 unknow
n exact 2
snp131_chr22:728 chr22 18807821 18807822 rs648663
0 + A A A/C genomic single
by-cluster,by-2hit-2allele 0 0intron exact 2
snp131_chr22:749 chr22 21609068 21609069 rs648663
0 + A A A/C genomic single
by-cluster,by-2hit-2allele 0 -
0 intron exact 2
snp132_chr22:728 chr22 18807821 18807822 rs648663
0 + A A A/C genomic single
by-cluster,by-2hit-2allele 0 0intron exact 2
MultipleAlignments 7
BCM-HGSC-SUB,BCMHGSC_JDW,GMI,SC_JCM,SC_SNP,SSAHASNP,TSC-CSHL, 0
snp132_chr22:749 chr22 21609068 21609069 rs648663
0 + A A A/C genomic single
by-cluster,by-2hit-2allele 0 0intron exact 2
MultipleAlignments 7
BCM-HGSC-SUB,BCMHGSC_JDW,GMI,SC_JCM,SC_SNP,SSAHASNP,TSC-CSHL, 0
________________________________
From: Sun, Ying [BSD] - HGD
Sent: Wed 6/8/2011 9:33 AM
To: Mary Goldman
Cc: [email protected]
Subject: RE: [Genome] snp132 chr14 download problem
It works perfectly now. Thanks.
Best,
Ying
________________________________
From: Mary Goldman [mailto:[email protected]]
Sent: Tue 6/7/2011 5:25 PM
To: Sun, Ying [BSD] - HGD
Cc: [email protected]
Subject: Re: [Genome] snp132 chr14 download problem
Hi Ying,
I'm sorry, but I was not able to reproduce your error. Is it possible
that the file was somehow corrupted during the download? Have you tried
to re-download the file?
If you are downloading an entire table, especially a large table such as
snp132, we highly recommend using our downloads server. Once you
download the file, you can separate the snp records into different files
based on chromosome.
To get to our downloads server, start at our homepage
(http://genome.ucsc.edu/) and click on "Downloads" in our blue side bar.
>From there, click on "Human" and scroll down to the section on hg19.
Click on the "Annotation Database" link and then click on
"snp132.txt.gz" link to download that file. The resulting link should
be: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz.
I hope this information is helpful. Please feel free to contact the
mail list again if you require further assistance.
Best,
Mary
------------------
Mary Goldman
UCSC Bioinformatics Group
On 6/7/11 2:32 PM, Sun, Ying [BSD] - HGD wrote:
> To whom it may concern,
>
> I am downloading dbsnp132 for all chromosomes at
> http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=197503545&clade=mammal&org=Human&db=hg19&hgta_group=varRep&hgta_track=snp132&hgta_table=0&hgta_regionType=range&position=chr14&hgta_outputType=primaryTable&hgta_outFileName=snp132_chr14,
> and everything works fine except chromosome 14. When I tried to gunzip it
> on Linux server, it always get error message "gunzip: snp132_chr14.gz:
> unexpected end of file". Please help to figure it out. Thanks a lot.
>
> Sincerely,
> Ying Sun
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