Learn · Next Generation Sequencing Technologies : Data Analysis and Applications
Lecture 8 of 60Week 2:
Lecture 08: Data Formats (Contd.)
Prof. Riddhiman Dhar · IIT Kharagpur
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- Next Generation Sequencing Technologies : Data Analysis and Applications, IIT Kharagpur (at NPTEL)
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- CC BY-NC-SA, as NPTEL states it. Non-commercial use only.
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All the lectures
- 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
- 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
- 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
- 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 & Quantification
- Lecture 35 : Transcript Abundance Quantification
- 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
- 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