Course10210509960 lectures
Next Generation Sequencing Technologies : Data Analysis and Applications
Prof. Riddhiman Dhar · IIT Kharagpur
About
Next Generation Sequencing (NGS) technologies have revolutionized Bioscience, Biotechnology and Medicine through generating unprecedented amount of data in the fields of genomics, transcriptomics and epigenomics. However, the data generated by NGS technologies has to be analyzed systematically to gain any meaningful information and to draw useful inferences. This course will describe the step-by-step process to analyze the data generated by NGS platforms along with relevant hands-on experience. The course will cover the analysis single nucleotide polymorphisms (SNPs) and indels. Further, the course will describe the complexities involved in the analysis of transcriptomic data in details. Finally, the course will end with an overview of other applications of the NGS technologies e.g., in genome assembly and epigenomics.
Intended audience: Students, Faculty and Industry professionals
Prerequisites: Basic knowledge of programming and statistics
Lectures
Week 1:
- Lecture 01: Introduction
- Lecture 02: Next Generation Sequencing Technologies - 454 Sequencing
- Lecture 03: Illumina Sequencing By Synthesis (SBS)
- Lecture 04 : Single Molecule Real Time (SMRT) Sequencing
- Lecture 05: Ion Torrent and Nanopore Sequencing
Week 2:
- Lecture 06: Sequencing Coverage,Quality Score and Experiment Design
- Lecture 07: Data Formats
- Lecture 08: Data Formats (Contd.)
- Lecture 09: Data Quality
- Lecture 10: Data QC and Trimming
Week 3:
- Lecture 11: Hands -on: Setting up the system
- Lesson 12 : Basic Shell Commands
- Lesson 13 : Data Download and Exploration
- Lesson 14 : Hands-on 1 - Data exploration and QC
- Lesson 15 : Hands-on 1 - Data QC and Trimming
Week 4:
- Lecture 16 : Read Mapping
- Lecture 17 : Mapping Algorithms
- Lecture 18 : Suffix tree-based mapping algorithm
- Lecture 19 : Burrows-Wheeler Transform (BWT)
- Lecture 20 : Read Mapping with BWT
Week 5 :
- Lecture 21: Bowtie2 tool
- Lecture 22 : Mapping reads with Bowtie2
- Lecture 23 : Bowtie2 output
- Lecture 24: SAM and BAM format
- Lecture 25 : SAM format: Alignment section
Week 6 :
- Lecture 26 : Variant Calling
- Lecture 27 : Calling SNP/SNVs and Indels
- Lecture 28 : Hands-on analysis : Variant Calling
- Lecture 29: VCF Files
- Lecture 30: Variant Annotation
Week 7
- Lecture 31 : Analysis of CNVs and SVs
- Lecture 32 : Introduction to RNA sequencing
- Lecture 33 : RNA-seq data processing pipeline
- Lecture 34 : Transcriptome Assembly & Quantification
- Lecture 35 : Transcript Abundance Quantification
Week 8 :
- Lecture 36 : Biases in RNA-seq experiments
- Lecture 37 : Data Normalization Methods
- Lecture 38 : Data Normalization Methods (Contd.)
- Lecture 39 : Differential Gene Expression (DGE) Analysis
- Lecture 40 : DGE analysis results and visualizations
Week 9 :
- Lecture 41 : Multiple hypothesis testing correction
- Lecture 42 : FDR correction and interpretation of DGE analysis results
- Lecture 43 : Functional Enrichment Analysis
- Lecture 44 : RNA-seq data analysis – Hands-on 2
- Lecture 45 : Hands-on 2: Setting up the system
Week 10 :
- Lecture 46 : Hands-on 2: Preliminary Data Analysis
- Lecture 47 : Sample Specific Bias Correction
- Lecture 48 : Differential Gene Expression Analysis I
- Lecture 49 : DGE Analysis with spike-ins
- Lecture 50 : DGE Analysis Results and Functional Enrichment Analysis
Week 11:
- Lecture 51 : Genome Assembly
- Lecture 52 : Shortest Common Superstring (SCS) assembly
- Lecture 53 : Overlap-Layout-Consensus (OLC) approach
- Lecture 54 : de Bruijn Graph (DBG) based assembly
- Lecture 55 : Assembly and Quality Control
Week 12 :
Syllabus and materials
At NPTEL, as the course publishes them.
Credits and licence
- Institution
- IIT Kharagpur
- Department
- Biotechnology
- Teacher
- Prof. Riddhiman Dhar
- Level
- Undergraduate
- Language
- English
- Subjects
- Biology
- Source
- NPTEL
- Licence
- CC BY-NC-SA, as NPTEL states it. Non-commercial use only. NPTEL's terms
- Attribution
- NPTEL states: "Distributed under Creative Commons Attribution-ShareAlike / CC BY - NC - SA", beside a BY-NC-SA badge.
- Who can watch
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