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Old 04-04-2012, 06:30 AM   #3
Senior Member
Location: Kansas City

Join Date: Mar 2008
Posts: 197

At UCSC, you can upload a custom track bed file, then use the table browser and do an intersection. You could also do this with galaxy "Fetch Sequences".

On the command line, you have a number of options... bedtools getfasta comes to mind.
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