MDO4
RNA-SEQ DATA ANALYSIS

<Training programs

Objectives :

Know how to analyze RNA-seq data.
Learn how to determine differentially expressed messenger RNAs and how to analyze expression results.

Level of trainees :

Technicians or Engineers (biologists or bioinformatician)
Knowledge in Bash and R is a plus for the practical exercises of this training

Duration and location :

• Duration : 28 hours over 4 days (as this training includes bioinformatics and biostatistics aspects, it is possible to split the different steps in order to target the specific needs of the trainees over a shorter period of time if required).
• Location: Soladis training center in Paris or Lyon (to consult the calendar, click on “Sign up”) or directly at your site (minimum of 4 people)

Training fee:

• At Soladis training center: 1950€ tax-free per trainee
• Other : Contact us for an offer adapted to your company.

Soladis invites you to participate in this training on the use of bioinformatics and biostatistics tools for the analysis of raw data, the determination of differentially expressed genes between two groups and the functional analysis of the results.

Training Schedule

REMINDER OF THE CONCEPTS ON THE BIOLOGY OF NGS

• The different types of sequencing (1st, 2nd and 3rd generation, paired or single-end)
• Sequencing depth vs. number of samples for reproducibility of analysis
• The different sequenced molecules and their interest

FROM FASTQ TO EXPRESSION MATRIX

• Choice of reference genome
• Quality control of sequencing outputs
• Alignment and essential post-alignment steps
• Post-alignment quality checks
• Counting readings and transformations

DIFFERENTIAL EXPRESSION ANALYSIS

• Data pre-processing
• Data visualization (PCA, PLS-DA, heatmap)
• Statistical modeling and signature definition of differentially expressed genes

FUNCTIONAL ANALYSIS OF THE RESULTS

• What is an expression signature?
• Reference databases
• Methods and input data
  • Fisher exact test
  • Gene set enrichment analysis
  • Single Sample Signature score

APPLICATIONS

• Examples of hands on study cases
• Use of public methods and pipelines (R and Bash languages)

Do not hesitate to contact us for more information about this training, which can be organized in our training center (dates provided on our website) or directly in your premises, according to your preferences.