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Question: How can I extract DNA sequence using a Perl script or R from UCSC if I have their coordinates?
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gravatar for dev831993
3.1 years ago by
dev831993 • 0
dev831993 • 0 wrote:

i have thousand  of coordinate region is in bed format like:

chr1    15903    15903
chr1    16808    16809
chr1    16840    16841
chr1    16948    16949
chr1    16956    16957
chr1    17019    17020
chr1    17221    17222
chr1    17384    17385
chr1    17397    17398
chr1    17537    17538

 

 
perl ucsc genome rowser bioinformatics R • 1.1k views
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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by dev831993 • 0
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gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

This can certainly be done using Galaxy with the tool Fetch Sequences: Extract Genomic DNA

But for help with general programming against the UCSC Table browser, review the documentation or contacing the UCSC support team would be best: http://genome.ucsc.edu

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
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