ComputerLab2b_Ernest_Feb3-2010

ComputerLab2b_Ernest_Feb3-2010 - COMPUTER LAB #2 Population...

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COMPUTER LAB #2 Population Genetics 2 Genotyping – collecting and assessing raw data from DNA analyzer Ecological Genetics PHR242 / ECL242 Feb 3 2010
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Announcements Homework 4 Due this Friday Feb 5 at 1pm to SmartSite Homework 5 on SmartSite by Friday 5pm For Monday Feb 8, read Ch 7 Guest lecture will also touch on the following concepts – feel free to look them up: Introgression, hybridization, SNPs, STRUCTURE (analysis of population structure) Quiz 1 returned in lab today; Key on SmartSite – Resources
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Genotyping software info In addition to those mentioned for microsat. genotyping earlier today (STRand- free, ABI Gene Mapper Software-not free) ABI company Web learning https://learn.appliedbiosystems.com/fragmentanalysis/ BROAD INSTITUTE SOFTWARE SNP typing, etc http://www.broad.mit.edu/tools/software.html
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LAST WEEK -PROOF-READING RAW GENOTYPE -DATA SET -MICROSATELLITE TOOLKIT “Summary Stats” – remember what they are? -INTRO TO GENEPOP Summary Stats, HWE, LE Summary statistics for population genetic data: Allele numbers and frequencies for each locus Heterozygosity (observed and expected) Data checking – are there replicate genotypes (individuals with the exact same alleles at all loci)?
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Pop Gen Data Analysis THE PROCESS Data generated in laboratory (more on that in future course labs) (TODAY and DNA lab) Proof read and digest the data (Today and Computer Lab 1) Archive the raw and polished data in a safe place (Computer Lab 1) Prepare input files for analysis software (Computer Lab 1) Run summary statistics (Computer Lab 1) Run statistical tests for Hardy-Weinberg Equilibrium and Linkage Equilibrium (TODAY) Set aside loci and individuals that have problem data (out of HWE or LE) – look at them later in case they represent interesting biology; rerun DNA analyses to
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This note was uploaded on 03/02/2010 for the course ECL 242 taught by Professor Holly during the Winter '10 term at UC Davis.

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ComputerLab2b_Ernest_Feb3-2010 - COMPUTER LAB #2 Population...

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