From a6e380119b90a11cc9466e8d0b481e501bf09bc6 Mon Sep 17 00:00:00 2001 From: drosofff Date: Fri, 15 Sep 2023 19:23:59 +0200 Subject: [PATCH 1/2] Work on IOC plan (9 weeks scheduled) --- docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md | 108 ++++++++++++++++---------- docs/bulk_RNAseq-IOC/links.md | 5 ++ mkdocs.yml | 3 +- 3 files changed, 75 insertions(+), 41 deletions(-) create mode 100644 docs/bulk_RNAseq-IOC/links.md diff --git a/docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md b/docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md index ef04473a..8f9cca17 100644 --- a/docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md +++ b/docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md @@ -1,54 +1,82 @@ -## Introduction to the IOC ARTbio 064: Bulk RNAseq Analyses +# Introduction to the IOC ARTbio 064: Bulk RNAseq Analyses **November 2023** In this Interactive Online Companionship, we will train to perform RNAseq analyses of Bulk RNAseq -### Program / Schedule - -### Week 1 - - **3-hours Zoom video-conference with** - - 1. Introduction of the Companions and Instructors (10 min) - - Presentation of the IOC general workflow (Scheme) (15 min) - - Presentation of the IOC tools (2 hours) - 1. Zoom (5 min) - - Starbio (5 min) - - Slack (10 min) - - GitHub (20 min) - - Psilo storage (15 min) - - Galaxy (65 min) - -
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  1. Import data from Psilo to Galaxy -
  2. Program of the week 2 -
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    1. Presentation of exercises with digital tools -
    2. presentation of pretreatment and metadata organisations and of related tasks to be done -
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- -### Week 2 -1. Question on Week 2 +## Program / Schedule + +### Week 1 - **3-hours Zoom video-conference** + + +1. Introduction of the Companions and Instructors (10 min) +- Presentation of the IOC general workflow (Scheme) (15 min) +- Presentation of the IOC tools (2 hours) + 1. Zoom (5 min) + - Starbio (5 min) + - Slack (10 min) + - GitHub (20 min) + - Psilo storage (15 min) + - Galaxy (65 min) + - Import data from Psilo to Galaxy +- Work Program of the week 1 - [Week-1 exercises]() + 1. Exercises with Slack (use of markdown, configuration, files, no-screen-shots, etc.) + - Exercises with GitHub (web version) + - Data upload in Galaxy, from Psilo + - Pretreatment (renaming and collections) and metadata organisations (and basic Galaxy manipulation) + +### Week 2 - **Quality control and References** +1. Question on Week 1 1. Data upload - 2. Quality control -- Program of Week 3 - 1. reference datasets (GTF, genome, subset, ucsc tables, ensembl Biomart) -### Week 3 -2. Questions on Week 2 + 2. Renaming, metadata organisation, collections + 3. Check point of data availability in Galaxy accounts +- Program of Week 2 - [Week-2 exercices]() + 1. Quality control (fastqc, multiQC, adapter trimming) + 2. reference datasets (Genome, GTF, subsets, ucsc tables, ensembl Biomart) +### Week 3 - **Read Mapping and Bam manipulation** +1. Questions on Week 2 1. reference - GTF manipulation -- Program of the Week 3 + - production of two parallel datasets, filtered/trimmed and not preatreated +- Program of the Week 3 [Week-3 exercices]() 1. Mapping and mappers 2. Inspection of Bam files + - InferExperiment for read orientations + +### Week 4 - **Counting Reads or Fragments** +1. Questions on Week 3 +- Program of the Week 4 [Week-4 exercices]() + 1. FeatureCount + 2. HTSeq-counts + 3. Count statistics and visualisations (side by side Scratchbook, R, etc) + +### Week 5 - **Statistical Analysis of Differential Gene Expression** +1. Questions on Week 4 +- Program of the Week 5 [Week-5 exercices]() + 1. DESeq2 + - EdgeR + - Volcano Plots, Waterfall plots + - RUVseq + +### Week 6 - **Gene Enrichment Analysis** +1. Questions on Week 5 +- Program of the Week 6 [Week-6 exercices]() + 1. GOseq + + +### Week 7 - **Gene Set Enrichment Analyses (GSEA)** +1. Questions on Week 6 +- Program of the Week 7 [Week-7 exercices]() + 1. GSEA + +### Week 8 - **Galaxy Workflows** +1. Questions on Week 7 +- Program of the Week 8 [Week-5 exercices]() + 1. building clean workflows to capture all details of the analysis -3. Analysis of the differential gene expression - 1. Count the number of reads per annotated gene - 2. Viewing datasets side by side using the Scratchbook - 3. Identification of the differentially expressed features - 4. Visualization of the differentially expressed genes - 5. Analysis of functional enrichment among the differentially expressed genes +### Week 9 - Presentations of the analyses by the companions +1. Questions on Week 8 (30 min max) +- 20 min presentations by the attendees Some parts of this IOC were inspired by [Reference-based RNAseq analysis](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html) diff --git a/docs/bulk_RNAseq-IOC/links.md b/docs/bulk_RNAseq-IOC/links.md new file mode 100644 index 00000000..d8d18953 --- /dev/null +++ b/docs/bulk_RNAseq-IOC/links.md @@ -0,0 +1,5 @@ +# External References + +- This IOC program was inspired by + [Reference-based RNAseq analysis](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html) + of the Galaxy Training Network (GTN) diff --git a/mkdocs.yml b/mkdocs.yml index 70b06124..0eac1e8f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -173,7 +173,8 @@ nav: - References: scRNAseq_basics/references.md - IOC on bulk RNAseq analysis: - - Introductive Session: bulk_RNAseq-IOC/01_IOC_RNAseq.md + - Introduction - Week-1: bulk_RNAseq-IOC/01_IOC_RNAseq.md + - External Materials: bulk_RNAseq-IOC/links.md - Introduction to Deep-seq Analysis: - INTRODUCTION: deepseq/index.md - Illumina sequencing: deepseq/illumina.md From b603bdf737e9d9b0606aa4c1effb11cf218bd611 Mon Sep 17 00:00:00 2001 From: drosofff Date: Fri, 15 Sep 2023 19:25:59 +0200 Subject: [PATCH 2/2] Update 01_IOC_RNAseq.md --- docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md b/docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md index 8f9cca17..3e1c5794 100644 --- a/docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md +++ b/docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md @@ -74,10 +74,6 @@ of Bulk RNAseq - Program of the Week 8 [Week-5 exercices]() 1. building clean workflows to capture all details of the analysis -### Week 9 - Presentations of the analyses by the companions +### Week 9 - **Presentations of the analyses by the companions** 1. Questions on Week 8 (30 min max) - 20 min presentations by the attendees - -Some parts of this IOC were inspired by -[Reference-based RNAseq analysis](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html) -of the Galaxy Training Network (GTN)