Genomics. Nolan C. Kane
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1 Genomics Nolan C. Kane
2 Course info s let me know if you are not getting them! me at Office hours by appointment and: Nolan: Tuesday 2-4, Ramaley N395 Kyle: Tues, Th 11:30-12:30, Ramaley N395
3 Genetics
4 Genetics
5 Genetics ACATTCGTTCGATGGCAACGGATTGGA TAACAGGCGCGCGCTTTGTTTTATTAT CCACATTATCAGCGGCATTATTGTTAT TATTGGCCCTCAGCGCTTTACCGCTCG CCCACGCGTCCGCCCGTGAATGCCGCG CGGAAAAGTCGCTTTCCACTAGATTGG CGTCCAGATTCGAGGAAATCCGTCAGC AGACGCATTCGCGCCCGTTCGGTCAGC ACTATGGCTAATAATCGTTCAAATCGT TAAAACCATAAAAATAATAATAATAAT TGCAATAACAATAAACATAGTAATAAT CGTAACGCTTACGAGCCTTTGATAGTG CCAAGGCAAGCGCAATCCAAGTATTCA
6 Genetics ACATTCGTTCGATGGCAACGGATTGGA TAACAGGCGCGCGCTTTGTTTTATTAT CCACATTATCAGCGGCATTATTGTTAT TATTGGCCCTCAGCGCTTTACCGCTCG CCCACGCGTCCGCCCGTGAATGCCGCG CGGAAAAGTCGCTTTCCACTAGATTGG CGTCCAGATTCGAGGAAATCCGTCAGC AGACGCATTCGCGCCCGTTCGGTCAGC ACTATGGCTAATAATCGTTCAAATCGT TAAAACCATAAAAATAATAATAATAAT TGCAATAACAATAAACATAGTAATAAT CGTAACGCTTACGAGCCTTTGATAGTG CCAAGGCAAGCGCAATCCAAGTATTCA
7 Genetics ACATTCGTTCGATGGCAACGGATTGGA TAACAGGCGCGCGCTTTGTTTTATTAT CCACATTATCAGCGGCATTATTGTTAT TATTGGCCCTCAGCGCTTTACCGCTCG CCCACGCGTCCGCCCGTGAATGCCGCG CGGAAAAGTCGCTTTCCACTAGATTGG CGTCCAGATTCGAGGAAATCCGTCAGC AGACGCATTCGCGCCCGTTCGGTCAGC ACTATGGCTAATAATCGTTCAAATCGT TAAAACCATAAAAATAATAATAATAAT TGCAATAACAATAAACATAGTAATAAT CGTAACGCTTACGAGCCTTTGATAGTG CCAAGGCAAGCGCAATCCAAGTATTCA
8 Genetics ACATTCGTTCGATGGCAACGGATTGGA TAACAGGCGCGCGCTTTGTTTTATTAT CCACATTATCAGCGGCATTATTGTTAT TATTGGCCCTCAGCGCTTTACCGCTCG CCCACGCGTCCGCCCGTGAATGCCGCG CGGAAAAGTCGCTTTCCACTAGATTGG CGTCCAGATTCGAGGAAATCCGTCAGC AGACGCATTCGCGCCCGTTCGGTCAGC ACTATGGCTAATAATCGTTCAAATCGT TAAAACCATAAAAATAATAATAATAAT TGCAATAACAATAAACATAGTAATAAT CGTAACGCTTACGAGCCTTTGATAGTG CCAAGGCAAGCGCAATCCAAGTATTCA
9 Genetics ACATTCGTTCGATGGCAACGGATTGGA TAACAGGCGCGCGCTTTGTTTTATTAT CCACATTATCAGCGGCATTATTGTTAT TATTGGCCCTCAGCGCTTTACCGCTCG CCCACGCGTCCGCCCGTGAATGCCGCG CGGAAAAGTCGCTTTCCACTAGATTGG CGTCCAGATTCGAGGAAATCCGTCAGC AGACGCATTCGCGCCCGTTCGGTCAGC ACTATGGCTAATAATCGTTCAAATCGT TAAAACCATAAAAATAATAATAATAAT TGCAATAACAATAAACATAGTAATAAT CGTAACGCTTACGAGCCTTTGATAGTG CCAAGGCAAGCGCAATCCAAGTATTCA
10 Genomics The study of whole genomes - All of the genes!
11 Genomics using bioinformatics to: Assemble new genomes De novo assembly reference-guided assembly Assess sequence variation Compare two genomes Compare unassembled reads from one genome to a reference of a different genotype Assess gene copy number
12 Why do we sequence genomes? Understand how life works All the genes, and how they are regulated Find important differences between species Evolutionary genomics Phylogenetics Identify genes associated with traits
13 'Complete' genomes on NCBI
14
15 Course goals Understand how genomic data is generated and analyzed Be able to identify sequence differences between genomes using next gen sequence Assemble at least 1 chloroplast or mitochondrial genome per student Annotate that genome and upload to genbank Compare genomes to ask evolutionary questions
16 Approach - Example genome - Each assemble our own genomes - Identify SNPs and INDELS from a reference - De novo assembly - genome annotation - Submit to NCBI - Comparative genomics
17 Unix, basic concepts Once you get used to the terminal, you will realize it is just another way of interacting with your computer, doing many of the same things you always do (open files, move files to new locations, copy files, delete files, etc.) and many more things, too.
18 To work efficiently in this environment, you need to keep track of: Where you are Who you are What files you need to use / make Where those files are What commands you can run How to run those commands
19 Unix, basic commands Basic terminal commands: ls list files and directories in your current location cd [new location] change to [new location] mkdir make a new directory cat show contents of a file on the screen Ctrl-C kills the current foreground process
20 Homework Day 2 Make sure you have access to a Unix / Linux machine! - install SSH and log onto my computers see instructions on AND me by midnight Monday night, with an update on your progress - Getting to know Unix list all of the Unix commands you have tried, and any problems Installing / testing SSH to log onto my computer
21 For class Tuesday Get comfortable with the basic commands The intro, and tutuorials 1-3 in: Read up on what is genomics:
22 In class Tuesday In class Tuesday we will be using a couple of programs: BWA - Samtools - And looking at an example dataset
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