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Bioinformatics Methods for Transcriptomics

kurs ist nicht verfügbar in Deutsch (Deutschland)

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Bioinformatics Methods for Transcriptomics

Dozent: Liliana Florea, PhD

4.893 bereits angemeldet

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Mehr erfahren

4 Module

Verschaffen Sie sich einen Einblick in ein Thema und lernen Sie die Grundlagen.

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2 Wochen zu vervollständigen

unter 10 Stunden pro Woche

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In Ihrem eigenen Lerntempo lernen

4 Module

Verschaffen Sie sich einen Einblick in ein Thema und lernen Sie die Grundlagen.

Stufe Mittel

Einige einschlägige Kenntnisse erforderlich

2 Wochen zu vervollständigen

unter 10 Stunden pro Woche

Flexibler Zeitplan

In Ihrem eigenen Lerntempo lernen

Kompetenzen, die Sie erwerben

Kategorie: Molecular, Cellular, and Microbiology
Kategorie: Linux Commands
Kategorie: Data Mapping
Kategorie: Molecular Biology
Kategorie: Bioinformatics
Kategorie: Statistical Methods
Kategorie: Statistical Analysis
Kategorie: Data Processing
Kategorie: Data Analysis Software
Kategorie: Analysis

Werkzeuge, die Sie lernen werden

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

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8 Aufgaben

Unterrichtet in Englisch

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In diesem Kurs gibt es 4 Module

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.

Moduldetails

Das ist alles enthalten

13 Videos5 Lektüren2 Aufgaben

13 VideosInsgesamt 106 Minuten

Course Introduction6 Minuten
Gene expression analysis of RNA-seq data3 Minuten
Step 1: Downloading and Preparing the Data9 Minuten
Step 2: Aligning the RNA-seq reads11 Minuten
Step 3: Assembling the Genes and Transcripts, Part 111 Minuten
Step 3: Assembling the Genes and Transcripts, Part 211 Minuten
Step 4: Determining the Differentially Expressed Genes, Part 13 Minuten
Step 4: Determining the Differentially Expressed Genes, Part 211 Minuten
Step 4: Determining the Differentially Expressed Genes, Part 36 Minuten
Step 4: Determining the Differentially Expressed Genes, Part 410 Minuten
Step 4: Determining the Differentially Expressed Genes, Part 513 Minuten
Step 5: Visualizing the Data, Part 14 Minuten
Step 5: Visualizing the Data, Part 29 Minuten

5 LektürenInsgesamt 45 Minuten

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

2 AufgabenInsgesamt 140 Minuten

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

Das ist alles enthalten

24 Videos2 Aufgaben

24 VideosInsgesamt 155 Minuten

Introduction to alternative splicing (AS) analysis, Part 19 Minuten
Introduction to alternative splicing (AS) analysis, Part 24 Minuten
Introduction to alternative splicing (AS) analysis, Part 32 Minuten
Step 1: Preparing the input data 2 Minuten
Step 2: Isoform-level analysis with Cuffdiff211 Minuten
Step 3: Event-level analysis with rMATS, Part 110 Minuten
Step 3: Event-level analysis with rMATS, Part 23 Minuten
Step 3: Event-level analysis with rMATS, Part 38 Minuten
Step 4A: Intron-level analysis with MntJULiP, Part 1 10 Minuten
Step 4A: Intron-level analysis with MntJULiP, Part 28 Minuten
Step 4A: Intron-level analysis with MntJULiP, Part 35 Minuten
Step 4A: Intron-level analysis with MntJULiP, Part 47 Minuten
Step 4B: Intron-level analysis with MntJULiP II8 Minuten
Step 5A: Intron retention analysis with IRFinder, Part 15 Minuten
Step 5A: Intron retention analysis with IRFinder, Part 22 Minuten
Step 5A: Intron retention analysis with IRFinder, Part 39 Minuten
Step 5B: Intron retention analysis with IRFinder II, Part 18 Minuten
Step 5B: Intron retention analysis with IRFinder II, Part 25 Minuten
Step 6A: AS visualization with IGV and Jutils I, Part 15 Minuten
Step 6A: AS visualization with IGV and Jutils I, Part 27 Minuten
Step 6B: AS visualization with Jutils II, Part 19 Minuten
Step 6B: AS visualization with Jutils II, Part 2 5 Minuten
Step 6B: AS visualization with Jutils II, Part 37 Minuten
Step 6B: AS visualization with Jutils II, Part 46 Minuten

2 AufgabenInsgesamt 140 Minuten

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

Das ist alles enthalten

14 Videos2 Aufgaben

14 VideosInsgesamt 105 Minuten

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

2 AufgabenInsgesamt 140 Minuten

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

Das ist alles enthalten

15 Videos2 Aufgaben

15 VideosInsgesamt 108 Minuten

Introduction to differential expression and splicing analysis with long read RNA sequencing8 Minuten
Preparing the data - a review4 Minuten
Differential gene and transcript expression (DESeq2), Part 112 Minuten
Differential gene and transcript expression (DESeq2), Part 29 Minuten
Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 111 Minuten
Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 29 Minuten
Differential splicing detection with short read tools (FLAIR diffSplice), Part 14 Minuten
Differential splicing detection with short read tools (FLAIR diffSplice), Part 28 Minuten
Differential splicing detection with short read tools (FLAIR diffSplice), Part 34 Minuten
Differential splicing detection with long read tools (1) (LIQA), Part 17 Minuten
Differential splicing detection with long read tools (1) (LIQA), Part 211 Minuten
Differential splicing detection with long read tools (2) (LIQA), Part 15 Minuten
Differential splicing detection with long read tools (2) (LIQA), Part 29 Minuten
Differential splicing detection with long read tools (2) (LIQA), Part 36 Minuten
Closing0 Minuten