hands-on tutorial
Reference-based RNA-Seq data analysis
The questions this addresses are:
- What are the steps to process RNA-Seq data?
- How to identify differentially expressed genes across multiple experimental conditions?
- What are the biological functions impacted by the differential expression of genes?
The objectives are:
- Check a sequence quality report generated by FastQC for RNA-Seq data
- Explain the principle and specificity of mapping of RNA-Seq data to an eukaryotic reference genome
- Select and run a state of the art mapping tool for RNA-Seq data
- Evaluate the quality of mapping results
- Describe the process to estimate the library strandness
- Estimate the number of reads per genes
- Explain the count normalization to perform before sample comparison
- Construct and run a differential gene expression analysis
- Analyze the DESeq2 output to identify, annotate and visualize differentially expressed genes
- Perform a gene ontology enrichment analysis
- Perform and visualize an enrichment analysis for KEGG pathways
Licence: Creative Commons Attribution 4.0 International
Keywords: QC, Transcriptomics, bulk, collections, cyoa, drosophila, rna-seq
Target audience: Students
Resource type: hands-on tutorial
Version: 93
Status: Active
Prerequisites:
- Introduction to Galaxy Analyses
- Mapping
- Quality Control
Learning objectives:
Check a sequence quality report generated by FastQC for RNA-Seq data
- Explain the principle and specificity of mapping of RNA-Seq data to an eukaryotic reference genome
- Select and run a state of the art mapping tool for RNA-Seq data
- Evaluate the quality of mapping results
- Describe the process to estimate the library strandness
- Estimate the number of reads per genes
- Explain the count normalization to perform before sample comparison
- Construct and run a differential gene expression analysis
- Analyze the DESeq2 output to identify, annotate and visualize differentially expressed genes
- Perform a gene ontology enrichment analysis
- Perform and visualize an enrichment analysis for KEGG pathways
Date modified: 2024-07-17
Date published: 2016-10-05
Contributors: Clea Siguret, Helena Rasche
Scientific topics: Transcriptomics
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