Lecture 1 - Introduction
Lecture 2 - Next Generation Sequencing Technologies - 454 Sequencing
Lecture 3 - Illumina Sequencing By Synthesis (SBS)
Lecture 4 - Single Molecule Real Time (SMRT) Sequencing
Lecture 5 - Ion Torrent and Nanopore Sequencing
Lecture 6 - Sequencing Coverage, Quality Score and Experiment Design
Lecture 7 - Data Formats
Lecture 8 - Data Formats (Continued...)
Lecture 9 - Data Quality
Lecture 10 - Data QC and Trimming
Lecture 11 - Hands-on: Setting up the system
Lecture 12 - Basic Shell Commands
Lecture 13 - Data Download and Exploration
Lecture 14 - Hands-on 1 - Data exploration and QC
Lecture 15 - Hands-on 1 - Data QC and Trimming
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
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
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
Lecture 31 - Analysis of CNVs and SVs
Lecture 32 - Introduction to RNA sequencing
Lecture 33 - RNA-seq data processing pipeline
Lecture 34 - Transcriptome Assembly and Quantification
Lecture 35 - Transcript Abundance Quantification
Lecture 36 - Biases in RNA-seq experiments
Lecture 37 - Data Normalization Methods
Lecture 38 - Data Normalization Methods (Continued...)
Lecture 39 - Differential Gene Expression (DGE) Analysis
Lecture 40 - DGE analysis results and visualizations
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
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
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
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
