To comprehend that the genome is data -- a set of instructions, and a record of history -- and to learn to use this information to test hypotheses.
Based on readings and discussions from the primary literature (free).
Through computational exercises in class and as assignments.
# simulate a chromosome from a coalescent tree_sequence tree_sequence = ms.simulate( sample_size=1000, length=int(1e5), Ne=int(1e5), mutation_rate=1e-9, recombination_rate=1e-10, random_seed=10, ) ## calculate linkage disequilibrium across the chromosome ldx = ms.LdCalculator(tree_sequence).get_r2_matrix()
What methods exist and when to choose one over another.
Learn to design, conduct, and analyze genomic experiments. By the end of class you should be able to:
1. Describe the structure of genomes; what information can be extracted.
2. Choose appropriate sequencing technologies for genomic experiments.
3. Analyze genomic data using computational methods.
Chapter 4 of free online
Initial sequencing and analysis of the human genome
(Lander et al. 2001)
Lines starting with hash (#) are only comments
# This is the general format of unix command line tools $ program -option1 -option2 target
# e.g., the 'pwd' program with no option or target $ pwd
I'll use a grey background to show the returned value
Always know where you are and where your files are.
# use the 'pwd' program with no option or target to ask where am I now? $ pwd # 'ls' shows the files and folders in a location (-l shows as a list) $ ls -l # the default target is here, but ls can be given a different target $ ls -l folder/ # 'cd' moves you to a new location. Now 'pwd' will say you are there. $ cd folder/
Your location (current directory) starts from / (the root) and is described by a nested set of directory names leading to your location.
# use 'pwd' program with no option or target to ask where am I now? $ pwd
We can make new directories and change our location.
# make a new directory $ mkdir genomics # change directory (move) into the new directory and run pwd again $ cd genomics $ pwd
There are many great tutorials, and google always has an answer. If you have no background in using the terminal then you should complete the Linux Command Line Tutorial on Codio, listed under the Courses tab on the left.