[Genome] Retrieve chromosomal positions between STS markers

[Brooke Rhead]

Hello James,

The table that contains this information is called 'stsMap', and the 
fields you will need to retrieve are 'chrom', 'chromStart', 'chromEnd' 
and 'name'.  For instance:

mysql> select chrom, chromStart, chromEnd, name from stsMap where name = 
'RH18061' or name = 'RH80175';
+-------+------------+----------+---------+
| chrom | chromStart | chromEnd | name    |
+-------+------------+----------+---------+
| chr7  |   27169002 | 27169152 | RH18061 |
| chr7  |   27172089 | 27172296 | RH80175 |
+-------+------------+----------+---------+
2 rows in set (0.01 sec)

 From here, you will need to select the the smallest chromStart and the 
biggest chromEnd from each pair to get the list of genomic regions.

In case you don't already have the instructions for accessing our public 
MySQL database, they are located here:
http://genome.ucsc.edu/FAQ/FAQdownloads#download29

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

-- 
Brooke Rhead
UCSC Genome Bioinformatics Group


Gao, James (NIH/NEI) [C] wrote:
> Hello,
> 
> In the human Genome browser, one can enter a pair of STS markers in the
> search term box, and the browser will display a region of the
> chromosome, such as entering RH18061;RH80175, the browser will display
> chr7:27,169,003-27,172,296. Here is my question: I have a list of pairs
> of these STS markers, can I use your MySQL database to retrieve those
> regions of chromosomes as displayed inside the browser?
> 
> Thank you.
> 
> James
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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