Bioinformatics Methods for Transcriptomics

Bioinformatics Methods for Transcriptomics

Instructor: Liliana Florea, PhD

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Assessments

8 assignments

Taught in English

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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 videosTotal 106 minutes

Course Introduction5 minutesPreview module
Gene expression analysis of RNA-seq data2 minutes
Step 1: Downloading and Preparing the Data9 minutes
Step 2: Aligning the RNA-seq reads11 minutes
Step 3: Assembling the Genes and Transcripts, Part 111 minutes
Step 3: Assembling the Genes and Transcripts, Part 210 minutes
Step 4: Determining the Differentially Expressed Genes, Part 13 minutes
Step 4: Determining the Differentially Expressed Genes, Part 211 minutes
Step 4: Determining the Differentially Expressed Genes, Part 36 minutes
Step 4: Determining the Differentially Expressed Genes, Part 410 minutes
Step 4: Determining the Differentially Expressed Genes, Part 512 minutes
Step 5: Visualizing the Data, Part 13 minutes
Step 5: Visualizing the Data, Part 28 minutes

5 readingsTotal 45 minutes

Course Syllabus10 minutes
Virtual Environment Setup10 minutes
Coursera Manual and Technical Support 10 minutes
List of software packages10 minutes
Forums for Module or Technical Questions5 minutes

2 assignmentsTotal 140 minutes

Module 1 Graded Project120 minutes
Checks for Understanding: Module 120 minutes

What's included

24 videos2 assignments

24 videosTotal 155 minutes

Introduction to alternative splicing (AS) analysis, Part 18 minutesPreview module
Introduction to alternative splicing (AS) analysis, Part 24 minutes
Introduction to alternative splicing (AS) analysis, Part 32 minutes
Step 1: Preparing the input data 2 minutes
Step 2: Isoform-level analysis with Cuffdiff211 minutes
Step 3: Event-level analysis with rMATS, Part 110 minutes
Step 3: Event-level analysis with rMATS, Part 23 minutes
Step 3: Event-level analysis with rMATS, Part 37 minutes
Step 4A: Intron-level analysis with MntJULiP, Part 1 9 minutes
Step 4A: Intron-level analysis with MntJULiP, Part 28 minutes
Step 4A: Intron-level analysis with MntJULiP, Part 35 minutes
Step 4A: Intron-level analysis with MntJULiP, Part 46 minutes
Step 4B: Intron-level analysis with MntJULiP II8 minutes
Step 5A: Intron retention analysis with IRFinder, Part 15 minutes
Step 5A: Intron retention analysis with IRFinder, Part 21 minute
Step 5A: Intron retention analysis with IRFinder, Part 38 minutes
Step 5B: Intron retention analysis with IRFinder II, Part 17 minutes
Step 5B: Intron retention analysis with IRFinder II, Part 25 minutes
Step 6A: AS visualization with IGV and Jutils I, Part 14 minutes
Step 6A: AS visualization with IGV and Jutils I, Part 27 minutes
Step 6B: AS visualization with Jutils II, Part 18 minutes
Step 6B: AS visualization with Jutils II, Part 2 4 minutes
Step 6B: AS visualization with Jutils II, Part 36 minutes
Step 6B: AS visualization with Jutils II, Part 46 minutes

2 assignmentsTotal 140 minutes

Module 2 Graded Project120 minutes
Checks for Understanding: Module 220 minutes

What's included

14 videos2 assignments

14 videosTotal 104 minutes

Introduction to transcriptomics with long RNA sequencing reads5 minutesPreview module
Preparing the input sequence data5 minutes
Aligning the long RNA sequencing reads, Part 18 minutes
Aligning the long RNA sequencing reads, Part 25 minutes
Building transcript models with FLAIR (align)10 minutes
Building transcript models with FLAIR7 minutes
Building transcript models with FLAIR (collapse), Part 16 minutes
Building transcript models with FLAIR (collapse), Part 210 minutes
Building transcript models with FLAIR (quantify) 5 minutes
Building transcript models with IsoQuant, Part 110 minutes
Building transcript models with IsoQuant, Part 25 minutes
Building transcript models with IsoQuant, Part 38 minutes
Visualizing transcript data with the IGV, Part 13 minutes
Visualizing transcript data with the IGV, Part 210 minutes

2 assignmentsTotal 140 minutes

Module 3 Graded Project120 minutes
Checks for Understanding: Module 320 minutes

What's included

15 videos2 assignments

15 videosTotal 107 minutes

Introduction to differential expression and splicing analysis with long read RNA sequencing7 minutesPreview module
Preparing the data - a review4 minutes
Differential gene and transcript expression (DESeq2), Part 111 minutes
Differential gene and transcript expression (DESeq2), Part 28 minutes
Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 111 minutes
Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 28 minutes
Differential splicing detection with short read tools (FLAIR diffSplice), Part 14 minutes
Differential splicing detection with short read tools (FLAIR diffSplice), Part 28 minutes
Differential splicing detection with short read tools (FLAIR diffSplice), Part 34 minutes
Differential splicing detection with long read tools (1) (LIQA), Part 17 minutes
Differential splicing detection with long read tools (1) (LIQA), Part 210 minutes
Differential splicing detection with long read tools (2) (LIQA), Part 15 minutes
Differential splicing detection with long read tools (2) (LIQA), Part 29 minutes
Differential splicing detection with long read tools (2) (LIQA), Part 35 minutes
Closing0 minutes