[Genome] Data download

[Brooke Rhead]

Hello Jason,

1.  The Table Browser can be used to download the genes in a particular 
region.  To use it, go to the Table Browser (the blue "Tables" link at 
the top of the page) and select the clade, genome, and assembly of 
interest.  Then choose "group: Genes and Gene Prediction Tracks", and 
the gene track you wish to use (Known Genes, RefSeq Genes, etc.).  Use 
the first table listed in the drop-down menu (the main table for a track 
is always listed first).  Be sure that "region: position" is selected, 
and that your region of interest is entered in the position box.  Choose 
"output format: selected fields from primary and related tables".  Enter 
a name for your output file if you want to download the results.  Hit 
"get output" and select the 'name' field, plus any additional fields you 
would like to output.  Hit "get output" again.  You should get a list of 
all of the genes in the region you specified.

2.  To search the Genome Browser using a list of chromosome regions, 
first create a custom track of the regions.  You will then be able to 
intersect your custom track with the gene track of interest using the 
Table Browser.  Help on creating a custom track is located here:

http://genome.ucsc.edu/goldenPath/help/customTrack.html

For a simple list of chromosome positions, use BED format, described here:

http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED

Once the custom track has been created, go the the Table Browser and 
select the gene track from which you wish to the retrieve gene names. 
Hit the "intersection: create" button and select your new custom track. 
  Choose one of the intersection options listed under "These 
combinations will maintain the gene/alignment structure (if any) of [the 
gene track]".  Hit "submit", then choose "output format: BED" and get 
the output.  You should get all records from the gene table you selected 
(including their positions) that intersect with your custom track.

I hope this information is helpful.  Please let us know if we can 
clarify any of the above, or if you have further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Lee, Jason Thanh wrote:
> Dear UCSC Genome Browser staff,
> 
>  
> 
> I have two questions, the first having higher priority.
> 
>  
> 
> 1.	After finding genes in a particular chromosome region, is there a
> simple way to download the list of genes found (eg. *.txt format)?
> 2.	Is there an automated way to search using a list of chromosome
> positions as input, and download the list of genes found per search item as
> output, keeping the chromosome_location-to-gene correlation?
> 
>  
> 
> Thank you in advance,
> 
>  
> 
> Jason Lee
> 
> UCLA/HHMI
> 
> 310-825-0169
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome