QTLcourse

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Contents

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Latest News

Greg Rebetzke has kindly provided his powerpoint slides. Download here. Also see [QTL Network 2.0]

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QTL Course Dinner

I've booked A Night In India, Shp 3/58 High St Toowong 4066 (07) 3217 7955 for 6:30 Wednesday night. It's BYO. See [www] for details.

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Software/Data Installation

During registration, we can install MapQTL, JoinMap and most (but not all) the other software to be used for the duration of the course. However, I would really appreciate you installing the software because

  1. there won't be enough time to install software for everyone and
  2. if there are problems installing it on your laptop then you will most likely miss out.

For details on installing software please see [here]. You also need the data for the exercises. Download here

Ideally you should have administrator rights in order to install packages during the course or to fix up anything that isn't working

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More Info

You can obtain a PDF page about the course here

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Course Details

  • Course: Linkage analysis and QTL mapping in plant species
  • Presenter: Christine Hackett [www], Principal Statistician, BioSS
  • Dates: Wednesday 25 - Friday 27 October 2006
  • Dates and Times:
    • Wednesday 25 October
      • 9am-10am: Registration
      • 10am - 5 pm: Linkage analysis and QTL mapping in inbreeding plant species
    • Thursday 26 October
      • 9am - 5pm: Linkage analysis and QTL mapping in outbreeding plant species
    • Friday 27 October
      • 9am-4pm: Advanced topics
  • Venue: Multi Media Training Facility 3.141, Queensland Bioscience Precinct, Building 80, University of Queensland, Building 80, St Lucia
    • Note: Please do not enter from the QBP reception area. Folk can enter from the ramp near the main lecture theatre.
  • Limited to 16 participants
  • Participants need to bring own computer which we will temporarily install JoinMap and MapQTL
  • Cost: The course is free. Morning and afternoon tea will be provided. Travel, meals and accomodation expenses will be met by participants.
  • Course notes
    • A comprehensive set of notes will be provided
  • Staying in Brisbane
    • Accomodation: PDF
    • Maps and info about UQ:
      • View map here, how to get to UQ here, and details of UQ traffic and parking here.
    • Trip Planner Transinfo web site
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Approximate course outline

  • Wed 25 October: methods for linkage analysis and QTL mapping in inbreeding plant species, using JoinMap and MapQTL
  • Thurs 26: methods for linkage analysis and QTL mapping in outbreeding species using JoinMap and MapQTL (will assume familiarity with material from previous day)
  • Friday 27: advanced QTL mapping for inbreeding species (discussing the strengths of different programmes - any participation welcome!) and time to work on your own data
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Computer Packages

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Essential

Please note that we will install MapQTL5 and JoinMap3 on your computer if you haven't already done so. Please ensure that you have Administrator rights in order for us to do this. However, I would really encourage you to have all this software installed and working in plenty of time before leaving home.

  • [JoinMap3]: Download the evaluation copy of JoinMap 3 (NOT 4!) [here]. The evaluation copy is very limited and so you should obtain the license file by emailing me
  • [MapQTL5]: Download the evaluation copy of MapQTL 5 [here]. The evaluation copy is very limited and so you should obtain the license file for the course by emailing me
  • [GENSTAT] is used for data checking, exploring etc. It looks like you can download a 30 day trial version. We haven't tried this. You will not be able to do this during the course.
    • Note: Presumably you may be able to obtain similar results with other statistical packages such as R or SAS. However, it will be much easier for everyone if you have GENSTAT installed on your laptop!
  • [R] and [Rqtl]: If you don't have R installed you can download the latest version from the [Brisbane] or [Melbourne] mirrors or the program setup file [here]. Once downloaded, run R-2.4.0-win32.exe to install. If you are on the internet you can install 'Rqtl' by choosing 'qtl' from the 'Install package(s) menu'. Otherwise you'll need to download it and install manually.
  • [PLABQTL] (PLant Breeding and Biology QTL) may be installed by grabbing PLABQTL.ZIP, unzipping it to a directory and adding the directory to your path. Its probably best to look at the readme file for more details. For viewing plots, which are postscript files, you'll need something like [ghostview].
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Recommended

  • [RECORD]: REcombination Counting and ORDering (RECORD) for the ordering of loci on genetic linkage maps. (DOS program ord.exe should be placed in a directory in your PATH).
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Potentially of interest

  • [MapChart]: Software for the graphical presentation of linkage maps and QTLs
  • [An Alphabetic List of Genetic Analysis Software]
  • [A Database of Genetic Analysis Software]
  • more R packages
    • bim Bayesian Interval Mapping Diagnostics
    • bqtl Bayesian QTL mapping toolkit
    • qtlbim QTL Bayesian Interval Mapping
    • qtlDesign Design of QTL experiments
    • LDheatmap Graphical display of pairwise linkage disequilibria between SNPs
    • ldDesign Design of experiments for detection of linkage disequilibrium
    • mapLD Linkage Disequilibrium Mapping
    • multic Quantitative linkage analysis tools using the variance components
    • MasterBayes Maximum Likelihood and Markov chain Monte Carlo methods for Pedigree Reconstruction, Analysis and Simulation
    • ape Analyses of Phylogenetics and Evolution
    • apTreeshape Analyses of Phylogenetic Treeshape
    • gap Genetic analysis package
    • genetics Population Genetics
    • ouch Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses
    • PHYLOGR Functions for phylogenetically based statistical analyses
    • popgen Statistical and Population Genetics
    • rmetasim An individual-based population genetic simulation environment
    • hapassoc Likelihood inference of trait associations with SNP haplotypes an
    • haplo.ccs Estimate Haplotype Relative Risks in Case-Control Data
    • haplo.stats Statistical Analysis of Haplotypes with Traits and Covariates whe
    • hapsim Haplotype Data Simulation
    • SNPassoc SNPs-based whole genome association studies
  • good editors for R
    • [emacs] with [ESS] if you like emacs on other operating systems
    • [Tinn-R] for a nice easy windows type editor that understands R
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Participants

  • List of Participants PDF
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