Hi Haojam,
When you go into the filter, I think setting you want for selecting
coding regions only is function ("func"). For SNP131 on hg19 the
options look like:
*Function*: Predicted functional role (/each variant may have more than
one functional role/)
* *Locus Region* - variation within 2000 bases of gene, but not in
transcript (near-gene-3, near-gene-5)
* *Coding - Synonymous* - no change in peptide for allele with
respect to reference assembly (coding-synon)
* *Coding - Non-Synonymous* - change in peptide for allele with
respect to reference assembly (nonsense, missense, frameshift,
cds-indel, coding-synonymy-unknown)
* *Untranslated* - variation in transcript, but not in coding region
interval (untranslated-3, untranslated-5)
* *Intron* - variation in intron, but not in first two or last two
bases of intron
* *Splice Site* - variation in first two or last two bases of intron
(splice-3, splice-5)
* *Unknown* - no known functional classification
(You can see a complete description of all the options by clicking
"describe table schema" on the table browser screen, to the right of the
selected table, and scrolling down about half-way. Just note that
different SNP versions might have slightly different settings.)
I think you will want to select (if using SNP131) function = "Coding -
Synonymous" and "Coding Non-Synonymous". Is that what you are looking for?
Just let us know if you have any additional questions.
--
Greg Roe
UCSC Genome Browser
On 1/7/11 7:29 PM, 하오잠 로 wrote:
> Mary Goldman
> UCSC Bioinformatics Group
>
> Dear,
> I would like to clarify for FILTER option available on the UCSC table browser
> site. Should I need to click single option only for CLASS field instead of
> ALL option which is represented with * AND for function fied should I click
> coding-synon, nonsense, missense, untranslated-3, untranslated-5 only instead
> of *. If I would like to get information for CoDing Sequences (CDS) only then
> should I click only for coding-synon, nonsense, missense. I would be glad for
> your assistance and kindness.
>
> Warm regards,
> Haojam Rocky
> Seoul National University College of Medicine
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