Program
Session 1
13/09/2023
Lectures:
- [15 minutes] General introduction of the lecture.
Practical:
- [60 minutes] Set up WSL config.
-
[90 minutes] Initiation to the basic command lines in Linux. Tutorial can be found at the following link.
Session 2
20/09/2023
Lectures:
- [30 minutes] Lecture 1 - Introduction to Genomics.
- [45 minutes] Lecture 2 - Introduction to Next Generation Sequencing (NGS).
Practical:
-
[90 minutes] Practical 1 - Assessing sequencing data quality (
fastqc).Session 3
27/09/2023
Practical:
- [45 minutes] Installation of
condaenvironment. - [120 minutes] Practical 1 - Assessing sequencing data quality (
fastqc,fastqscreen,multiqc).
Session 4
02/10/2023
Lectures:
- [60 minutes] Lecture 3 - Sequence alignment
Practical:
- [15 minutes] Practical 1 - Assessing sequencing data quality (small conclusion).
- [90 minutes] Practical 2 - Sequence alignment (
cutadpatandbowtie2).
Session 5
04/10/2023
Lectures:
- [60 minutes] Lecture 4 - Transcriptomics.
Practical:
- [105 minutes] Practical 2 - Sequence alignment & introduction to IGV (
samtoolsandIGV).
Session 6
09/10/2023
Lectures:
- [60 minutes] Lecture 5 - DESeq2 : A software to normalize RNA sequencing counts data.
- [45 minutes] Lecture 6 - Overview of the bacteriophage biology.
Practical:
- [60 minutes] Practical 2 - Phage temporal regulation - introduction to IGV.
Session 7
11/10/2023
Lectures:
- [30 minutes] Lecture 5 - DESeq2 : A software to normalize RNA sequencing counts data.
Practical:
- [135 minutes] Practical 3 - Introduction to DESeq2 analysis.
Session 8
25/10/2023
Lectures:
- [60 minutes] Lecture 7 - Introduction to Single Cell RNAseq.
- [45 minutes] Lecture 8 - Introduction to ChIP-seq.
- [15 minutes] Lecture 9 - What is a peak in ChIP-seq ?
- [45 minutes] Lecture 10 - Assessing chromatin accessibility.
Practical:
Session 9
06/11/2023
Practical - Exam
- [30 minutes] Explication of the project and examples.
-
[150 minutes] Personnal work by group of two to work by group of two on the open question.
Session 10
22/11/2023
Practical - Exam
- [15 minutes] Written Exam (Quiz)
- [150 minutes] Personnal work by group of two to work by group of two on the open question.