From 4604c7316c97b1da2d1006daacd61867f275f570 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 7 Apr 2022 14:32:41 -0500
Subject: Create DOL-mapping.gmi

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 issues/DOL-mapping.gmi | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 issues/DOL-mapping.gmi

(limited to 'issues')

diff --git a/issues/DOL-mapping.gmi b/issues/DOL-mapping.gmi
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+# DOL group mapping issues
+
+## Tags
+
+* assigned: zsloan
+* type: bug
+* priority: medium
+* status: in-progress
+* keywords: mapping
+
+## Description
+
+After generating the genotype files for the Diversity Outbred Lung (DOL) group for Jacco Boon*, there were issues with GEMMA and R/qtl mapping.
+
+These issues seem to have been caused by a couple mitochondrial markers having a position of 0Mb. For now, I've addressed this by changing their positions to 0.000001 and 0.000002Mb respectively.
+
+There's also an issue that hasn't been addressed yet with displaying mitochondrial markers in the GN2 figure. GEMMA is outputting the results, so I suspect this is because mitochondria isn't included in the databased list of chromosomes associated with Mouse.
+
+* as described here - https://kbroman.org/qtl2/pages/prep_do_data.html
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