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Methods Mol Biol. 2009;573:175-88. doi: 10.1007/978-1-60761-247-6_10.

Quantitative trait locus analysis using J/qtl.

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The Jackson Laboratory, Bar Harbor, ME, USA.


Quantitative trait locus (QTL) analysis is a statistical method to link phenotypes with regions of the genome that affect the phenotypes in a mapping population. R/qtl is a powerful statistical program commonly used for analyzing rodent QTL crosses, but R/qtl is a command line program that can be difficult for novice users to run. J/qtl was developed as an R/qtl graphical user interface that enables even novice users to utilize R/qtl for QTL analyses. In this chapter, we describe the process for analyzing rodent cross data with J/qtl, including data formatting, data quality control, main scan QTL analysis, pair scan QTL analysis, and multiple regression modeling; this information should enable new users to identify QTL affecting phenotypes of interest within their rodent cross datasets.

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