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CompLabNGS

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.

Setting up your environment

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.

Course timeline

Week Date Topic Slides Data Class/HW assignments
1 03/11/2024 Introduction to NGS and Genomics Lecture 1 Setting up your environment
2 10/11/2024 Introduction to Linux and the command line Lecture 2 Data Class assignment 1
3 17/11/2024 NGS data quality control and pre-processing Lecture 3 Data Class assignment 2

Large files

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

Roadmap to final grade of 100

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: 02.03.2025

Download the data | git clone

If you wish to pull data and material hosted in this GitHub 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.

Then, to clone the repository, use the following command:

git clone https://github.com/hadasvolk/CompLabNGS.git

From now on, you can use git pull to get the latest version of the repository. E.g., you can run:

cd CompLabNGS
git pull

Do it every time you want to get the latest version of the repository.