[Genome] Query about knownGenes tables at http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/

[Archana Thakkapallayil]

Hello Lalitha,

I am not sure what you are looking at. But, I don't see anything wrong 
with the IDs in the tables that you've mentioned. They all have values 
from uc001 ... uc004.

To view a description for a specific table, select that table in the 
Table Browser, then click the "describe table schema" button (if you 
know the table name and want to bypass the group/track settings, simply 
set group="All Tables", then select your table from the table list). On 
this page you can also see which other tables are related to the one 
currently in use and via which identifier, under the section "Connected 
Tables and Joining Fields".

hg18.knownToLocusLink.name (via knownGene.name)
hg18.knownToRefSeq.name (via knownGene.name)

I hope this information is helpful to you.  If you have further 
questions, please do not hesitate to contact us again.

Regards,

Archana
UCSC Genome Bioiformatics Group

Viswanath, Lalitha (NIH/NCI) [C] wrote:
> Hi
>
> I am looking for detailed documentation regarding the following 3 tables
>
> knownGenes.txt.gz
>
> knownToLocusLink.txt.gz
>
> knownToRefSeq.txt.gz
>
> at  http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/
>
> I am using the first file to get chromosomal starts and stops for genes
> from UCSC's Genome Browser and the latter 2 to get the mappings to
> corresponding RefSeq and Entrez Gene Ids.
>
> Strangely I find that none of the UCSC Ids in the first file find a
> mention in the other two files??
>
> The ids in the first file are prefixed uc007xxxx while the ids in the
> other two files are prefixed uc004xxx.
>
>  
>
> Any inputs on understanding the above better would be helpful.
>
>  
>
> Hoping to hear further
>
> Thanks
>
> Lalitha
>
>  
>
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