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Program

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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 conda environment.
• [120 minutes] Practical 1 - Assessing sequencing data quality (fastqc, fastqscreen, multiqc).

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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 (cutadpat and bowtie2).

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Session 5

04/10/2023

Lectures:

• [60 minutes] Lecture 4 - Transcriptomics.

  Practical:

• [105 minutes] Practical 2 - Sequence alignment & introduction to IGV (samtools and IGV).

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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.

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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.

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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:

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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.