Bioinformatics Methods for Transcriptomics
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Bioinformatics Methods for Transcriptomics
Instructor: Liliana Florea, PhD
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There are 4 modules in this course
This course will cover bioinformatics methods for analyzing transcriptomic RNA sequencing data generated with the short read (RNA-seq) and long read (PacBio, ONT) sequencing. In its four modules, the course addresses the core transcriptomics questions: What are the genes and transcripts expressed in a given sample or condition of an experiment?, What are their expression levels?, and What are the differences in gene expression and splicing patterns between conditions? It provides hands-on instruction on how to use popular and/or emerging tools such as STAR, PsiCLASS, DESeq2, rMATS, MntJULiP, Minimap2 and IsoQuant. This is an intermediate level course, and assumes basic knowledge on using command line bioinformatics tools in a Unix-type environment.
What's included
13 videos5 readings2 assignments
13 videos•Total 106 minutes
- Course Introduction•6 minutes
- Gene expression analysis of RNA-seq data•3 minutes
- Step 1: Downloading and Preparing the Data•9 minutes
- Step 2: Aligning the RNA-seq reads•11 minutes
- Step 3: Assembling the Genes and Transcripts, Part 1•11 minutes
- Step 3: Assembling the Genes and Transcripts, Part 2•11 minutes
- Step 4: Determining the Differentially Expressed Genes, Part 1•3 minutes
- Step 4: Determining the Differentially Expressed Genes, Part 2•11 minutes
- Step 4: Determining the Differentially Expressed Genes, Part 3•6 minutes
- Step 4: Determining the Differentially Expressed Genes, Part 4•10 minutes
- Step 4: Determining the Differentially Expressed Genes, Part 5•13 minutes
- Step 5: Visualizing the Data, Part 1•4 minutes
- Step 5: Visualizing the Data, Part 2•9 minutes
5 readings•Total 45 minutes
- Course Syllabus•10 minutes
- Virtual Environment Setup•10 minutes
- Coursera Manual and Technical Support •10 minutes
- List of software packages•10 minutes
- Forums for Module or Technical Questions•5 minutes
2 assignments•Total 140 minutes
- Checks for Understanding: Module 1•20 minutes
- Module 1 Graded Project•120 minutes
What's included
24 videos2 assignments
24 videos•Total 155 minutes
- Introduction to alternative splicing (AS) analysis, Part 1•9 minutes
- Introduction to alternative splicing (AS) analysis, Part 2•4 minutes
- Introduction to alternative splicing (AS) analysis, Part 3•2 minutes
- Step 1: Preparing the input data •2 minutes
- Step 2: Isoform-level analysis with Cuffdiff2•11 minutes
- Step 3: Event-level analysis with rMATS, Part 1•10 minutes
- Step 3: Event-level analysis with rMATS, Part 2•3 minutes
- Step 3: Event-level analysis with rMATS, Part 3•8 minutes
- Step 4A: Intron-level analysis with MntJULiP, Part 1 •10 minutes
- Step 4A: Intron-level analysis with MntJULiP, Part 2•8 minutes
- Step 4A: Intron-level analysis with MntJULiP, Part 3•5 minutes
- Step 4A: Intron-level analysis with MntJULiP, Part 4•7 minutes
- Step 4B: Intron-level analysis with MntJULiP II•8 minutes
- Step 5A: Intron retention analysis with IRFinder, Part 1•5 minutes
- Step 5A: Intron retention analysis with IRFinder, Part 2•2 minutes
- Step 5A: Intron retention analysis with IRFinder, Part 3•9 minutes
- Step 5B: Intron retention analysis with IRFinder II, Part 1•8 minutes
- Step 5B: Intron retention analysis with IRFinder II, Part 2•5 minutes
- Step 6A: AS visualization with IGV and Jutils I, Part 1•5 minutes
- Step 6A: AS visualization with IGV and Jutils I, Part 2•7 minutes
- Step 6B: AS visualization with Jutils II, Part 1•9 minutes
- Step 6B: AS visualization with Jutils II, Part 2 •5 minutes
- Step 6B: AS visualization with Jutils II, Part 3•7 minutes
- Step 6B: AS visualization with Jutils II, Part 4•6 minutes
2 assignments•Total 140 minutes
- Checks for Understanding: Module 2•20 minutes
- Module 2 Graded Project•120 minutes
What's included
14 videos2 assignments
14 videos•Total 105 minutes
- Introduction to transcriptomics with long RNA sequencing reads•6 minutes
- Preparing the input sequence data•5 minutes
- Aligning the long RNA sequencing reads, Part 1•9 minutes
- Aligning the long RNA sequencing reads, Part 2•6 minutes
- Building transcript models with FLAIR (align)•10 minutes
- Building transcript models with FLAIR•8 minutes
- Building transcript models with FLAIR (collapse), Part 1•7 minutes
- Building transcript models with FLAIR (collapse), Part 2•11 minutes
- Building transcript models with FLAIR (quantify) •6 minutes
- Building transcript models with IsoQuant, Part 1•10 minutes
- Building transcript models with IsoQuant, Part 2•5 minutes
- Building transcript models with IsoQuant, Part 3•9 minutes
- Visualizing transcript data with the IGV, Part 1•4 minutes
- Visualizing transcript data with the IGV, Part 2•10 minutes
2 assignments•Total 140 minutes
- Checks for Understanding: Module 3•20 minutes
- Module 3 Graded Project•120 minutes
What's included
15 videos2 assignments
15 videos•Total 108 minutes
- Introduction to differential expression and splicing analysis with long read RNA sequencing•8 minutes
- Preparing the data - a review•4 minutes
- Differential gene and transcript expression (DESeq2), Part 1•12 minutes
- Differential gene and transcript expression (DESeq2), Part 2•9 minutes
- Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 1•11 minutes
- Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 2•9 minutes
- Differential splicing detection with short read tools (FLAIR diffSplice), Part 1•4 minutes
- Differential splicing detection with short read tools (FLAIR diffSplice), Part 2•8 minutes
- Differential splicing detection with short read tools (FLAIR diffSplice), Part 3•4 minutes
- Differential splicing detection with long read tools (1) (LIQA), Part 1•7 minutes
- Differential splicing detection with long read tools (1) (LIQA), Part 2•11 minutes
- Differential splicing detection with long read tools (2) (LIQA), Part 1•5 minutes
- Differential splicing detection with long read tools (2) (LIQA), Part 2•9 minutes
- Differential splicing detection with long read tools (2) (LIQA), Part 3•6 minutes
- Closing•0 minutes
2 assignments•Total 140 minutes
- Checks for Understanding: Module 4•20 minutes
- Module 4 Graded Project•120 minutes
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