Question: How To Get The Sequence Of A Genomic Region From Ucsc?
4
gravatar for Giovanni M Dall'Olio
10.7 years ago by
Barcelona, Spain
Giovanni M Dall'Olio420 wrote:

Let's say I want to download the fasta sequence of the region chr1:100000..200000 from the UCSC browser. How do you do that? I can't find a button to 'export to fasta' in the UCSC genome browser. I think that the solution is to click on one of the tracks displayed, but I am not sure of which. If I go to the Tables section, I can't find a table with the fasta sequences among the many.

sequence ucsc fasta • 1.1k views
ADD COMMENTlink modified 10.7 years ago by Jane ♦♦ 0 • written 10.7 years ago by Giovanni M Dall'Olio420
3
gravatar for Pierre Lindenbaum
10.7 years ago by
France
Pierre Lindenbaum140 wrote:

Use the DAS server:

http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr1:100000,200000

ADD COMMENTlink written 10.7 years ago by Pierre Lindenbaum140
2
gravatar for István Albert
10.7 years ago by
István Albert ♦♦ 310
University Park
István Albert ♦♦ 310 wrote:

The Genome Browser is for visualization.

To get data in many formats use the UCSC Table Browser then select the output format of your choice.

You may also need to select the right group and track to get the data you want.

ADD COMMENTlink written 10.7 years ago by István Albert ♦♦ 310
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