[Genome] Batch extraction

[Kayla Smith]

Hello Mitchell,

The "define regions" option is working correctly.  If you are retrieving 
refGenes, there is not information about which part of the defined 
regions each refGene is in.

What you can do is to make a Custom Track of your regions then intersect 
that with refGene using the Table Browser.   Here are instructions for 
making a Custom Track:
http://genome.ucsc.edu/goldenPath/help/customTrack.html

Finally, if that doesn't give you a detailed enough intersection, let me 
recommend that you use the Galaxy tool:
http://main.g2.bx.psu.edu/

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

Mike Mitchell wrote:
> Hello!,
> 
> I have a list of 90+ regions for which I would would like to extract data
> from the TableBrowser.
> 
> If I upload these regions into the "define regions" interface the data I get
> back doesn't (seem to) identify which region any particular RefGene is
> within.
> 
> I could c&p each region into the tablebrowser and do the 90+ searches in
> turn, but that will be laborious (and no doubt prone to human error.) Is
> there a way to do a "batch" TableBrowser query? Or is there a better tool I
> could use?
> 
> Thanks in advance for your time and help.
>