Skip to content

Provisional Program / Schedule

In this Interactive Online Companionship which will be held from January 8th to March 18th, 2024, we will train to perform RNAseq analyses of Bulk RNAseq

Week 0 - 3-hours Zoom video-conference

  1. Introduction of the Companions and Instructors (10 min)
  2. Presentation of the IOC general workflow (Scheme) (15 min)
  3. Presentation of the IOC tools (2 hours)
    1. Zoom (5 min)
    2. Starbio (5 min)
    3. Slack (10 min)
    4. GitHub (20 min)
    5. Psilo storage (15 min)
    6. Galaxy (65 min)
    7. Import data from Psilo to Galaxy
  4. Work Program of the week 0 - Week-0 exercises
    1. Exercises with Slack (use of markdown, configuration, files, no-screen-shots, etc.)
    2. Exercises with GitHub (web version)
    3. Data upload in Galaxy, from Psilo
    4. Pretreatment (renaming and collections) and metadata organisations (and basic Galaxy manipulation)

Week 1 - Quality control and References

  1. Question on Week 0
    1. Data upload
    2. Renaming, metadata organisation, collections
    3. Check point of data availability in Galaxy accounts
  2. Program of Week 1 - Week-1 exercices
    1. Quality control (fastqc, multiQC, adapter trimming)
    2. reference datasets (Genome, GTF, subsets, ucsc tables, ensembl Biomart)

Week 2 - Read Mapping and Bam manipulation

  1. Questions on Week 1
    1. reference
    2. GTF manipulation
    3. production of two parallel datasets, filtered/trimmed and not preatreated
  2. Program of the Week 2 Week-2 exercices
    1. Mapping and mappers
    2. Inspection of Bam files
    3. InferExperiment for read orientations

Week 3 - Counting Reads or Fragments

  1. Questions on Week 2
  2. Program of the Week 3 Week-3 exercices
    1. FeatureCount
    2. HTSeq-counts
    3. Count statistics and visualisations (side by side Scratchbook, R, etc)

Week 4 - Statistical Analysis of Differential Gene Expression

  1. Questions on Week 3
  2. Program of the Week 4 Week-4 exercices
    1. DESeq2
    2. EdgeR
    3. Volcano Plots, Waterfall plots
    4. RUVseq

Week 5 - Gene Enrichment Analysis

  1. Questions on Week 4
  2. Program of the Week 5 Week-5 exercices
    1. GOseq

Week 6 - Gene Set Enrichment Analyses (GSEA)

  1. Questions on Week 5
  2. Program of the Week 6 Week-6 exercices
    1. GSEA

Week 7 - Galaxy Workflows

  1. Questions on Week 6
  2. Program of the Week 7 Week-7 exercices
    1. building clean workflows to capture all details of the analysis

Week 8 - Presentations of the analyses by the companions

  1. Questions on Week 7 (30 min max)
  2. 20 min presentations by the attendees