Genetics 711/811 | Bioinformatics and GenomicsΒΆ
Course Description:
The methods, applications, and implications of genomics–the analysis of whole genomes. Microbial, plant and animal genomics are addressed, as well as medical, ethical and legal implications. The lab provides exposure and experience on a range of bioinformatics approaches–the computer applications used in genome analysis.
Contact Information for Professor Matthew MacManes
- Office: 189 Rudman Hall
- Phone: 603-862-4052
- Email (preferred): Matthew.MacManes@unh.edu
- Twitter: @macmanes
- Office hours: Tues/Fri 8-10AM in 189 Rudman, or by appt. Schedule at http://genomebio.org/office-hours/
Lecture: MWF 11:10-12:00PM Rudman G89
Lab: Friday 3:10-5:00PM Hewitt 301
- Lecture Materials.
Welcome Lecture 0
BLAST Lecture 1
Lecture 4Sept15
Lecture 9Sept15
Alignment Lecture 14Sept15
Alignment Lecture 16Sept15
- HMM Info
HMM/fastQ Lecture 21Sept15
Illumina Lecture 23Sept15
Trimming Lecture 28Sept15
Error Correction Lecture 30Sept15
Lecture 5Oct15
Lecture 7Oct15
A few more Review Slides
Lecture 15Oct15 Diginorm
Lecture 19Oct15
Lecture 21Oct15
Lecture 28Oct15
Lecture 4Nov15
Lecture 6Nov15
Lecture 13Nov15
Lecture 16Nov15
Lecture 18Nov15
Lecture 30Nov15
Final Lecture
- Lab lessons
- Getting Started with UNIX
Launch an EC2 Instance
- Lab 04Sept15: Lab 0: BLAST
- Lab 11Sept15: Lab 1: Alignment
- Lab 11Sept15: Github and Why use Git
- Lab 18Sept15: Lab3 : HMMER
- Lab 25Sept15: Lab4: Processing fastQ
- Lab 2Oct15: Lab5: Trimming fastQ
- Lab 15Oct15: Lab 5: khmer
- Lab 23Oct15: Lab 6: setup for transcriptome assembly
- Lab 30Oct15: Lab 7: Analyze transcriptome
- Lab 6Nov15: Lab 8: Read Mapping
- Lab 13Nov15: Lab 9: Gene Expression
- Reading
- Lab reading for 9/4. PCFB Chapter 4: See Matt if you don’t have a copy of the book yet.
Week 1 lecture Reading
- Reading Week2: Google BLAST and Type 1 error, Benjamini-Hochberg correction.
Week 2 lecture/lab Reading
We will continue with this material in week 3 as well.- Lab reading for 9/14. PCFB Chapter 5
- HMM Reading for week of 9/21
- Lab reading for 9/21. PCFB Chapter 6
- Read Trimming
Error Correction
- Another error correction paper
- Khmer paper
- Skewer paper
- Digital Normalization
- Assembly
- Everything you wanted to know about everything (CS oriented)
- Seq Assembly Demystified
- How to Assemble a genome videos
- Full Bioinformatics video series
- BUSCO paper
- Explain Shell
- Command Line Bootcamp
- Homework
- HOMEWORK 1 Due date: 18Sept15
- HW2 Due date: 30Oct15
Exams
- Yikes!!!: MOCK EXAM 1
- Utter Panic: MOCK EXAM 2
- Practice for exam2: EXAM 2 -Practice
- The real deal exam 2: EXAM 2