Quantitative Trait Locus Analysis Using J/qtl

Part of the Methods in Molecular Biology™ book series (MIMB, volume 573)


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.

Key words

Quantitative trait locus analysis QTL 



We are grateful to Sharon Tsaih and Qian Li for preparing the summary table and several figures.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.The Jackson LaboratoryBar HarborUSA
  2. 2.Novartis Institutes for BioMedical Research and Novartis Pharmaceutical CorporationEast HanoverUSA

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