Genetics 220 - Computational Analysis of High Throughput Biological Data

Lectures

• Course Outline
• UNIX I: Introduction to Command Line
• UNIX II: Running programs in UNIX and Git Tutorial and in PDF
• UNIX III: Tools for data processing and see data links
• UCR Biocluster: Running jobs with Slurm on HPC - Charles Forsyth
• Python 1 - Variables, running, cmdline, strings, math
• Python 2 - Logic, loops, lists, iterator - Sawyer Masonjones
• Python 3 - Input/Output files
• Python 4 - Dictionaries, Arrays, functions
• Python 4 - Regular Expressions
• Python 5 - Libraries, packages, BioPython
• Bioinformatics 1 - cmdline BLAST
• Bioinformatics 2 - Short reads, alignment, stats, SNPs
• Bioinformatics 3 - RNAseq
• Data Plotting and brief intro to R graphics
• Comparative genomics, Orthologs
• Phylogenetics

Homework

1. Homework 1 [PDF] [Markdown text]
2. Homework 2 [PDF] [Markdown text]
3. Homework 3 [PDF] [Markdown text]
4. Homework 4 [PDF] [Markdown text]

Resources

• Git Tutorial HTML PDF
• SSH Tutorial HTML PDF
• Code snippetes - code examples. Worked up while developing the lectures