hands-on tutorial
Hands-on for 'Reference-based RNA-Seq data analysis' tutorial
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: transcriptomics, bulk, rna-seq, collections, drosophila, QC, cyoa
Target audience: Students
Resource type: hands-on tutorial
Contributors: Anika Erxleben, Bérénice Batut, Clemens Blank, Lucille Delisle, Mallory Freeberg, Maria Doyle, Mo Heydarian, Nicola Soranzo, Pavankumar Videm, Peter van Heusden
Scientific topics: Transcriptomics
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