Informatics for RNA-Seq Analysis
Course Objectives
High-throughput sequencing of RNA libraries (RNA-seq) has become increasingly common and largely supplanted gene microarrays for transcriptome profiling. When processed appropriately, RNA-seq data has the potential to provide a considerably more detailed view of the transcriptome. The CBW has developed a 2-day course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. The tutorials are designed as self-contained units that include example data (Illumina paired-end RNA-seq data) and detailed instructions for installation of all required bioinformatics tools (TopHat, Cufflinks, etc.). De novo assembly of transcripts is not covered.
Participants will gain practical experience and skills to be able to:
- Align RNA-seq data to a reference genome (required)
- Estimate known gene and transcript expression
- Perform differential expression analysis
- Discover novel isoforms
- Visualize and summarize the output of RNA-seq analyses
Course Material
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Module 1 - Introduction to Cloud Computing
Instructor(s): Obi Griffith
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Module 2 - Introduction to RNA sequencing and analysis
Instructor(s): Malachi Griffith
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Module 3 - RNA-seq alignment and visualization
Instructor(s): Fouad Yousif
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Module 4 - Expression and Differential Expression
Instructor(s): Obi Griffith
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Module 5 - Isoform Discovery and Alternate Expression
Instructor(s): Malachi Griffith
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Module 6 - Reference free analysis
Instructor(s): Obi Griffith
Presentation file(s):