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katz...@gmail.com

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Nov 4, 2020, 2:44:03 PM11/4/20
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I'd like to confirm something I've always assumed. The map positions for the DO genotype files linked to at https://kbroman.org/qtl2/pages/prep_do_data.html are, and have been since that web page went up, grcm38 (mm10). Right?

Karl Broman

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Nov 4, 2020, 5:17:24 PM11/4/20
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I'd recommend using the maps from here: https://github.com/kbroman/MUGAarrays
Positions in mm10.

karl

David K

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Nov 4, 2020, 8:06:29 PM11/4/20
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Very good. I will swap out my DO geno files. However, could you also confirm the build for the DO data linked to on the qtl2 page? Thanks very much. 

David

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David C. Katz, Ph.D.
Postdoctoral Fellow
Benedikt Hallgrimsson Lab
University of Calgary

Research Associate
Department of Anthropology
University of California, Davis

David K

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Nov 4, 2020, 8:08:29 PM11/4/20
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... in relation to some old results. 

On Wed, Nov 4, 2020 at 3:17 PM Karl Broman <kbr...@gmail.com> wrote:
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Karl Broman

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Nov 4, 2020, 9:09:41 PM11/4/20
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The source of the files is explained in the document: ftp://ftp.jax.org/MUGA
I believe the physical positions are mm10, but I'm not positive.

The readme file there says
"Thanks to Andrew Morgan of UNC for providing the marker locations at:"


If you go to http://csbio.unc.edu/MUGA/ there's a table that suggests that the muga and megamuga locations are in mm9 and the gigamuga locations are mm10.

karl

David K

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Nov 4, 2020, 11:45:39 PM11/4/20
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Thanks, Karl. 

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