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Old 12-20-2011, 09:55 AM   #1
david.tamborero
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Default which human Reference genome to use

I guess it is a very stupid question, but there is a difference between using the hg19 reference genome vs the GRCh37?

I want to align reads by using bfast, and I am wondering whether to use USCS vs NCBI data could change the resulting coordinates of the aligned reads (the .sam file).

Thank you very much!
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Old 12-20-2011, 10:08 AM   #2
GenoMax
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David: see this link for a discussion about hg19 vs GRCh37 (and specific patches) issue at UCSC. https://lists.soe.ucsc.edu/pipermail...st/026824.html
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Old 12-21-2011, 08:59 AM   #3
david.tamborero
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Thank you for your answer, GenoMax.

So if I've understood it well (I'm novice in these kind of things, sorry!) the hg19 is the same (so the same nucleotides in the same positions!) to the first version of GRCh37, but the hg19 is not updated according to the further revised GRCh37 versions (I've noticed five patches)?

Thanks again...
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Old 12-22-2011, 06:22 AM   #4
GenoMax
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That is my understanding.

Document the exact version you used for analysis, where you got the data from and that should be adequate.

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Originally Posted by david.tamborero View Post
Thank you for your answer, GenoMax.

So if I've understood it well (I'm novice in these kind of things, sorry!) the hg19 is the same (so the same nucleotides in the same positions!) to the first version of GRCh37, but the hg19 is not updated according to the further revised GRCh37 versions (I've noticed five patches)?

Thanks again...
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Old 12-22-2011, 06:27 AM   #5
david.tamborero
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Thank you, I'll do it.
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