Bioinformatics Methods for Transcriptomics

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Bioinformatics Methods for Transcriptomics

Instructeur : Liliana Florea, PhD

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4 modules

Obtenez un aperçu d'un sujet et apprenez les principes fondamentaux.

niveau Intermédiaire

Certaines connaissances prérequises

2 semaines à compléter

à 10 heures par semaine

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Apprenez à votre propre rythme

4 modules

Obtenez un aperçu d'un sujet et apprenez les principes fondamentaux.

niveau Intermédiaire

Certaines connaissances prérequises

2 semaines à compléter

à 10 heures par semaine

Planning flexible

Apprenez à votre propre rythme

Compétences que vous acquerrez

Catégorie : Data Analysis Software
Catégorie : Linux Commands
Catégorie : Molecular Biology
Catégorie : Bioinformatics
Catégorie : Analysis
Catégorie : Statistical Methods
Catégorie : Statistical Analysis
Catégorie : Data Processing

Outils que vous découvrirez

Catégorie : Linux
Catégorie : Command-Line Interface
Catégorie : R (Software)

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8 devoirs

Enseigné en Anglais

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Il y a 4 modules dans ce cours

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.

Inclus

13 vidéos5 lectures2 devoirs

13 vidéosTotal 106 minutes

Course Introduction6 minutes
Gene expression analysis of RNA-seq data3 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 211 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 513 minutes
Step 5: Visualizing the Data, Part 14 minutes
Step 5: Visualizing the Data, Part 29 minutes

5 lecturesTotal 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 devoirsTotal 140 minutes

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

Inclus

24 vidéos2 devoirs

24 vidéosTotal 155 minutes

Introduction to alternative splicing (AS) analysis, Part 19 minutes
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 38 minutes
Step 4A: Intron-level analysis with MntJULiP, Part 1 10 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 47 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 22 minutes
Step 5A: Intron retention analysis with IRFinder, Part 39 minutes
Step 5B: Intron retention analysis with IRFinder II, Part 18 minutes
Step 5B: Intron retention analysis with IRFinder II, Part 25 minutes
Step 6A: AS visualization with IGV and Jutils I, Part 15 minutes
Step 6A: AS visualization with IGV and Jutils I, Part 27 minutes
Step 6B: AS visualization with Jutils II, Part 19 minutes
Step 6B: AS visualization with Jutils II, Part 2 5 minutes
Step 6B: AS visualization with Jutils II, Part 37 minutes
Step 6B: AS visualization with Jutils II, Part 46 minutes

2 devoirsTotal 140 minutes

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

Inclus

14 vidéos2 devoirs

14 vidéosTotal 105 minutes

Introduction to transcriptomics with long RNA sequencing reads6 minutes
Preparing the input sequence data5 minutes
Aligning the long RNA sequencing reads, Part 19 minutes
Aligning the long RNA sequencing reads, Part 26 minutes
Building transcript models with FLAIR (align)10 minutes
Building transcript models with FLAIR8 minutes
Building transcript models with FLAIR (collapse), Part 17 minutes
Building transcript models with FLAIR (collapse), Part 211 minutes
Building transcript models with FLAIR (quantify) 6 minutes
Building transcript models with IsoQuant, Part 110 minutes
Building transcript models with IsoQuant, Part 25 minutes
Building transcript models with IsoQuant, Part 39 minutes
Visualizing transcript data with the IGV, Part 14 minutes
Visualizing transcript data with the IGV, Part 210 minutes

2 devoirsTotal 140 minutes

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

Inclus

15 vidéos2 devoirs

15 vidéosTotal 108 minutes

Introduction to differential expression and splicing analysis with long read RNA sequencing8 minutes
Preparing the data - a review4 minutes
Differential gene and transcript expression (DESeq2), Part 112 minutes
Differential gene and transcript expression (DESeq2), Part 29 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 29 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 211 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 36 minutes
Closing0 minutes

2 devoirsTotal 140 minutes

Checks for Understanding: Module 420 minutes
Module 4 Graded Project120 minutes

Instructeur

Liliana Florea, PhD

Johns Hopkins University

2 Cours37 219 apprenants

Offert par

Johns Hopkins University

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