Sequence download from UCSC hg19

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Janine Lamb

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Dec 13, 2012, 7:26:05 AM12/13/12

to gen...@soe.ucsc.edu

Hi,

Is it still possible to download sequence data for a specific region from the UCSC browser e.g. if i browse to a specific chr location, then want to download the sequence data?
I've tried going through table utilities/ downloads, and looked on old versions of the browser, but am failing.

I only have ~5 100bp regions.

Thanks

Janine.

*******************************************************************************
Janine Lamb DPhil.|Senior Lecturer in Complex Human Genetics/Genomics |Director, MRes Translational Medicine |Centre for Integrated Genomic Medical Research (CIGMR) |Manchester Academic Health Science Centre |Rm 2.722 Stopford Building |The University of Manchester |Oxford Road |Manchester |M13 9PT
Tel: 0161 275 1619 |Fax: 0161 275 1617| Email: Janin...@manchester.ac.uk

CIGMR:http://www.medicine.manchester.ac.uk/genomics/
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Pauline Fujita

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Dec 13, 2012, 10:18:38 PM12/13/12

to Janine Lamb, gen...@soe.ucsc.edu

Hello Janine,

You have 2 options for this task. If you want to retrieve sequence for
a single region you can input your coordinates into the browser and
from the main browser page select "View" then "DNA" from the top bar.
This will take you to the "get DNA" tool and will retrieve sequence
for whatever region you were viewing in the browser.

If you would like to retrieve DNA for multiple regions at once the
best way is to make a BED format custom track of your regions, then
use the Table Browser to extract sequence from your custom track. For
more info on that see this FAQ:

http://genome.ucsc.edu/FAQ/FAQdownloads.html#download32

Since you are only looking to get sequence for 5 regions, option B
from the FAQ is probably more suited to your needs.

If you have further questions please feel free to contact the mailing
list again at gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu