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Old 10-11-2011, 11:50 AM   #9
Heisman
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Location: St. Louis

Join Date: Dec 2010
Posts: 535
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Oh, that's a different question, haha.

When you create your reference sequence and make your fasta headers, I suggest making the header the genomic coordinates of the specific interval. Then, if one portion of your reference sequence is named "chr1:45673-58472" and you call a SNP at:

chr1:45673-58472 564

You can know the mutation is at chr1: (45673 + 564 -1) (be careful not to be off by one). So, even if your programming skills aren't good, you can put this in excel and convert everything to the genomic coordinates.

Last edited by Heisman; 10-11-2011 at 11:58 AM.
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