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Question: Extracting Sequences with coordinates directly from the human genome(hg19), using biopython or Galaxy
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gravatar for manasalankac
3.9 years ago by
manasalankac • 0
United States
manasalankac • 0 wrote:

Hi! I am not able to enter the build number in 'Fetch Sequences for intervals in' section in the Extract Genomic DNA window. How should I do that? I am new to using Galaxy. I wanted to extract reference sequences of human genome (hg19) with coordinates and use it to fetch snippets of sequences in Biopython  (earlier I was trying to do this directly using Biopython -- by using the Entrez.efetch function and somehow access and import just parts of the human genome, for about >3000 IDs --couldn't find a solution, and so I moved on to Galaxy.) Any suggestions?
galaxy human genome sequences • 2.1k views
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modified 3.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.9 years ago by manasalankac • 0
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gravatar for Jennifer Hillman Jackson
3.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Assign the metadata attribute "database" to the dataset with the sequence coordinates to be extracted (bed or gtf dataset). Use the pencil icon to do this, the option to assign a reference genome is on the first tab in the form set that will come up in the middle panel. Type "hg19" into the build list search to locate the genome, then save and try again, leaving the Extract tool form setting "Source for Genomic Data:" as " Locally cached". 

Hopefully this helps, Jen, Galaxy team

 
ADD COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k
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