{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

ComputerLab2b_Ernest_Feb3-2010

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

Info icon This preview shows pages 1–6. Sign up to view the full content.

View Full Document Right Arrow Icon
COMPUTER LAB #2 Population Genetics 2 Genotyping – collecting and assessing raw data from DNA analyzer Assessing data for HWE & LE Ecological Genetics PHR242 / ECL242 Feb 3 2010
Image of page 1

Info icon This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
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
Image of page 2
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
Image of page 3

Info icon This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
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)?
Image of page 4
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
Image of page 5

Info icon This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Image of page 6
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern