Welcome to TAU Life Sciences - Computational Lab in Next Generation Sequencing and Genomics Data Analysis - 0411358701
Course material will be updated weekly prior to our Sunday session. Make sure you grub necessary slides, data and class/HW assignments from the relevant directory.
Course announcements and HW submissions will be delivered via the course's Moodle site only!
Please use the Issues tab above to ask questions and report problems. Your questions will be answered by the course staff and/or your fellow students. Please refrain from sending us emails regarding course-related issues. Your questions and our answers will be visible to all students. This way, we can avoid duplicate questions and you can benefit from the questions and answers of your fellow students.
Our course is all about hands-on experience with NGS data analysis. You'll need to set yourself up with a Unix-based environment. Please follow the instructions on 0-SettingUp for possible solutions to this task.
| Week | Date | Topic | Slides | Data | Class/HW assignments |
|---|---|---|---|---|---|
| 1 | 31/12/2023 | Introduction to NGS and Genomics | Lecture 1 | Setting up your environment | |
| 2 | 07/01/2024 | Introduction to Linux and the command line | Lecture 2 | Data | Class assignment 1 |
| 3 | 14/01/2024 | NGS data quality control and pre-processing | Lecture 3 | Data | Class assignment 2 |
| 4 | 21/01/2024 | "Catching Up" week | |||
| 5 | 28/01/2024 | Sequence mapping part I | Lecture 4 | Data | Class assignment 3 |
| 6 | 04/02/2024 | Sequence mapping part II | Lecture 5 | Data | Class assignment 4 |
| 7 | 11/02/2024 | Variant calling | Lecture 6 | Data | Class assignment 5 |
| 8 | 18/02/2024 | Assembly | Lecture 7 | Data | Class assignment 6 |
| 9 | 25/02/2024 | RNA-Seq I | Lecture 8 | Data | Class assignment 7 |
| 10 | 03/03/2024 | Python for Bioinformatics | Lecture 9 | Data | Class assignment 8 |
| 11 | 10/03/2024 | RNA-Seq II | Lecture 10 | Data | Class assignment 9 |
Some of the files in this repository are large and cannot be viewed directly in the browser. These files are accesible in a Google Drive folder. You can access the folder here
30 points - Class assignments
- Starting on lesson 2
- Two weeks to complete each assignment and submit via Moodle
- Pass only - no partial credit
- Must submit at least 8 assignments to pass the course
70 points - Final project
- Can be done in pairs
- Submission deadline: 01.05.2024
If you wish to pull all data from this repo automatically and not download each file individually, you can use git to clone the entire repository to your local machine.
Make sure you have git installed by running git --version. If you don't have it installed, you can download it from here. Or simply use the sudo apt install git command if you are using a Ubuntu-based system.
You'll also need git-lfs to pull the large files. You can download it from here.
For Ubuntu do
curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash
sudo apt install git-lfsThen, to clone the repository, use the following command:
git clone https://github.com/hadasvolk/CompLabNGS.gitFrom now on, you can use git pull to get the latest version of the repository. E.g., you can run:
cd CompLabNGS
git pullDo it every time you want to get the latest version of the repository.