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Introduction to Data Science with Python
4.3174 ratingsLearn the concepts and techniques that make up the foundation of data science and machine learning.
IIT Kharagpur via NPTEL
Next Generation Sequencing Technologies : Data Analysis And Applications
Overview
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.
Syllabus 12
- 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 :
- Lecture 56 : Applications of NGS in Epigenomics
- Lecture 57 : Detecting DNA Methylations
- Lecture 58 : Genome-wide Transcription Factor (TF) Binding Sites
- Lecture 59 : Chromatin Accessibility
- Lecture 60 : Genome Organization in 3D
Advantages and disadvantages
Advantages
- Taught by IIT and IISc professors, and it follows the Indian university syllabus closely.
- All videos and assignments are free on NPTEL and SWAYAM.
- The certificate is recognised by many Indian universities for credit transfer and by GATE aspirants.
- Great for GATE and semester exam preparation.
- Taught by Indian Institute of Technology Kharagpur, one of the strongest names in its field.
- Completely free.
- Self-paced: start any time.
- A clear syllabus (12 parts) you can see before you start.
Disadvantages
- The certificate needs a proctored exam at a centre, which has a fee.
- Recorded classroom lectures: thorough, but slower than made-for-online courses.
- New runs start on fixed dates (January and July).
- Learning is free, but the certificate costs money.
Some points apply to every course of this kind; see how we rank.
Free to learn
- Free: Every video and assignment is free on NPTEL and SWAYAM. Enrol when the next run opens.
- Certificate: Optional. It needs a proctored exam at a centre, which has a fee.
Before you start
Basic knowledge of programming and statistics
Taught by
- Prof. Riddhiman DharIIT Kharagpur
Indian Institute of Technology Kharagpur is in Tier 1: world-leading universities and India's top institutes of our institution ranking (95/100).
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