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Bioinformatics Methods for Transcriptomics · LearnSpace
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Bioinformatics Methods for Transcriptomics

Курс от Johns Hopkins University
Средний≈ 18 чАнглийский
О курсеНавыкиПрограммаПреподаватели

О курсе

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.

Навыки, которые вы освоите

BioinformaticsStatistical AnalysisStatistical MethodsData Analysis SoftwareCommand-Line InterfaceLinux CommandsAnalysisR (Software)Data ProcessingMolecular BiologyLinux

Программа курса

4 модулей · 79 учебных материалов

01Module 1: Course Introduction and Gene expression analysis of RNA-seq data20 материалов

Welcome to Command Line Tools for Transcriptomics

Course IntroductionВидеоCourse SyllabusЧтениеVirtual Environment SetupЧтениеCoursera Manual and Technical Support Чтение

Gene expression analysis of RNA-seq data

Учитесь у экспертов

Liliana Florea, PhD

Associate Professor

Bioinformatics Methods for Transcriptomics
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Обучение на Coursera

≈ 18 ч

4 модулей

Язык: Английский

Часть программы вашего университета
Gene expression analysis of RNA-seq dataВидео

Step 1: Downloading and Preparing the Data

Step 1: Downloading and Preparing the DataВидео

Step 2: Aligning the RNA-seq reads

Step 2: Aligning the RNA-seq readsВидео

Step 3: Assembling the Genes and Transcripts

Step 3: Assembling the Genes and Transcripts, Part 1ВидеоStep 3: Assembling the Genes and Transcripts, Part 2Видео

Step 4: Determining the Differentially Expressed Genes

Step 4: Determining the Differentially Expressed Genes, Part 1ВидеоStep 4: Determining the Differentially Expressed Genes, Part 2ВидеоStep 4: Determining the Differentially Expressed Genes, Part 3ВидеоStep 4: Determining the Differentially Expressed Genes, Part 4ВидеоStep 4: Determining the Differentially Expressed Genes, Part 5Видео

Step 5: Visualizing the Data

Step 5: Visualizing the Data, Part 1ВидеоStep 5: Visualizing the Data, Part 2Видео

Checks for Understanding

Checks for Understanding: Module 1Задание

Graded Project: Module 1

List of software packagesЧтениеForums for Module or Technical QuestionsЧтениеModule 1 Graded ProjectЗадание
02Module 2: Alternative splicing analysis of RNA-seq data26 материалов

Introduction to alternative splicing (AS) analysis

Introduction to alternative splicing (AS) analysis, Part 1ВидеоIntroduction to alternative splicing (AS) analysis, Part 2ВидеоIntroduction to alternative splicing (AS) analysis, Part 3Видео

Step 1: Preparing the input data

Step 1: Preparing the input data Видео

Step 2: Isoform-level analysis with Cuffdiff2

Step 2: Isoform-level analysis with Cuffdiff2Видео

Step 3: Event-level analysis with rMATS

Step 3: Event-level analysis with rMATS, Part 1ВидеоStep 3: Event-level analysis with rMATS, Part 2ВидеоStep 3: Event-level analysis with rMATS, Part 3Видео

Step 4A: Intron-level analysis with MntJULiP I

Step 4A: Intron-level analysis with MntJULiP, Part 1 ВидеоStep 4A: Intron-level analysis with MntJULiP, Part 2ВидеоStep 4A: Intron-level analysis with MntJULiP, Part 3ВидеоStep 4A: Intron-level analysis with MntJULiP, Part 4Видео

Step 4B: Intron-level analysis with MntJULiP II

Step 4B: Intron-level analysis with MntJULiP IIВидео

Step 5A: Intron retention analysis with IRFinder I

Step 5A: Intron retention analysis with IRFinder, Part 1ВидеоStep 5A: Intron retention analysis with IRFinder, Part 2ВидеоStep 5A: Intron retention analysis with IRFinder, Part 3Видео

Step 5B: Intron retention analysis with IRFinder II

Step 5B: Intron retention analysis with IRFinder II, Part 1ВидеоStep 5B: Intron retention analysis with IRFinder II, Part 2Видео

Step 6A: AS visualization with IGV and Jutils I

Step 6A: AS visualization with IGV and Jutils I, Part 1ВидеоStep 6A: AS visualization with IGV and Jutils I, Part 2Видео

Step 6B: AS visualization with IGV and Jutils II

Step 6B: AS visualization with Jutils II, Part 1ВидеоStep 6B: AS visualization with Jutils II, Part 2 ВидеоStep 6B: AS visualization with Jutils II, Part 3ВидеоStep 6B: AS visualization with Jutils II, Part 4Видео

Checks for Understanding

Checks for Understanding: Module 2Задание

Graded Project: Module 2

Module 2 Graded ProjectЗадание
03Module 3: Transcriptome reconstruction with long RNA sequencing reads16 материалов

Introduction to transcriptomics with long RNA sequencing reads

Introduction to transcriptomics with long RNA sequencing readsВидео

Preparing the input sequence data

Preparing the input sequence dataВидео

Aligning the long RNA sequencing reads

Aligning the long RNA sequencing reads, Part 1ВидеоAligning the long RNA sequencing reads, Part 2Видео

Building transcript models with FLAIR (align)

Building transcript models with FLAIR (align)Видео

Building transcript models with FLAIR (correct)

Building transcript models with FLAIRВидео

Building transcript models with FLAIR (collapse)

Building transcript models with FLAIR (collapse), Part 1ВидеоBuilding transcript models with FLAIR (collapse), Part 2Видео

Building transcript models with FLAIR (quantify)

Building transcript models with FLAIR (quantify) Видео

Building transcript models with IsoQuant

Building transcript models with IsoQuant, Part 1ВидеоBuilding transcript models with IsoQuant, Part 2ВидеоBuilding transcript models with IsoQuant, Part 3Видео

Visualizing transcript data with the IGV

Visualizing transcript data with the IGV, Part 1ВидеоVisualizing transcript data with the IGV, Part 2Видео

Checks for Understanding

Checks for Understanding: Module 3Задание

Graded Project: Module 3

Module 3 Graded ProjectЗадание
04Module 4: Differential expression and differential splicing analysis with long RNA sequencing reads17 материалов

Introduction to differential expression and splicing analysis with long read RNA sequencing

Introduction to differential expression and splicing analysis with long read RNA sequencingВидео

Preparing the data - a review

Preparing the data - a reviewВидео

Differential gene and transcript expression (DESeq2)

Differential gene and transcript expression (DESeq2), Part 1ВидеоDifferential gene and transcript expression (DESeq2), Part 2Видео

Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2)

Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 1ВидеоDifferential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 2Видео

Differential splicing detection with short read tools (FLAIR diffSplice)

Differential splicing detection with short read tools (FLAIR diffSplice), Part 1ВидеоDifferential splicing detection with short read tools (FLAIR diffSplice), Part 2ВидеоDifferential splicing detection with short read tools (FLAIR diffSplice), Part 3Видео

Differential splicing detection with long read tools (1) (LIQA)

Differential splicing detection with long read tools (1) (LIQA), Part 1ВидеоDifferential splicing detection with long read tools (1) (LIQA), Part 2Видео

Differential splicing detection with long read tools (2) (LIQA)

Differential splicing detection with long read tools (2) (LIQA), Part 1ВидеоDifferential splicing detection with long read tools (2) (LIQA), Part 2ВидеоDifferential splicing detection with long read tools (2) (LIQA), Part 3Видео

Checks for Understanding

Checks for Understanding: Module 4Задание

Graded Project: Module 4

Module 4 Graded ProjectЗадание

Closing

ClosingВидео