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NGS course (G788/I590) - Yunlong Liu Lab

The video collections for the 2011 lectures are now available at Youtube and Youku. The slides can also be downloaded.  

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MGEN-G788 (INFO-I590) Introduction to Next Generation Sequencing

Time: 3PM-6PM, Fridays (Fall 2013 Semester)

Location: HS 1110 (Map)

Course materials:

  • Course materials are available in the oncourse system. If you need access, please email the course TA (Haoyu Cheng: for access. If you do NOT have an IU university ID, please acquire an IU guest user ID following instruction:
  • Podcast of the lectures is now available in the oncourse system.



Understanding the basic principles of next generation sequencing technology. This includes basic biological applications, basics in data processing, statistical and informatics theories in data analysis, advantages, limitations, and assumptions of different methodologies, and biological interpretation of the results. 

Expected outcomes:

For School of Informatics students: know how to do the analysis

  • Understand the basics of biological questions
  • Implement different analysis tools (such as alignment, alternative splicing, variant call, ...)
  • Fully understand the standard data structure; capable of retrieve relevant information throug basic programming
  • Understand statistical/computational models to solve different biological questions

For School of Medicine students: know how to interpret the results, and know how to creatively design an experiment using NGS technology

  • Understand the basics of informatics theories
  • Understand the standard data structure (what information is included in each file)
  • Appreciate the advantages, limitations, and assumptions of standard stantistical/bioinformatics methods
  • Interpret the analysis results
  • Creativly design an experiement for solving the problem of your own research interest

For faculty and staff sitting in the class: due to the expected heterogeneous nature of the class, some of the lectures may provide more informatics/statisitics details than you need. If you have any suggestions on the class contents, please feel free to contact me at

If you want to officially audit the class, please read and follow the IUPUI audit policy on the IUPUI Office of Registrar. If no credit is needed, please just drop me a message indicating you are interested in auditing.


*** Lab tour to the Center for Medical Genomics will be separately arranged





Aug 23

Overview of next generation sequencing technology

  • What is NGS?
  • Platform overview
  • Biological applications
  • Basic concepts
  • Recent scientific breakthroughs using NGS technology
  • Class overview


Aug 30

Data processing

  • Analysis workflow
  • Sequence quality evaluation
  • Alignment theories
  • Data formats
  • Data visualization


Sep 6

DNA-seq I

  • What is genetic variations?
  • States of the genetic research for complex disease prior to high throughput sequencing
  • NGS and genetics of complex disease (etiology)
  • NGS and personal genome sequencing
  • Experimental considerations
    • Whole genome sequencing
    • Target sequencing
    • Pool sequencing


Sep 13


 DNA-seq II – Bioinformatics topics for DNA-seq data analysis

  • Sequencing mappability
  • Refined alignment
  • Base quality recalibration
  • Variants identification for
    • Diploid genome
    • Pooled DNA sequencing
    • Cancer genome
  • Variation recalibration
  • Pair-ends – identifying structure variants


Sep 20


Guest Lecture - Drs. Howard Edenberg and Xiaoling Xuei

  • Basics of library preparation protocols for SOLiD platform
  • Tour to the Center for Medical Genomics sequencing facility


Sep 27

Guest lecture – Dr. Tatiana Foroud

  • Exome sequencing in FIA and PD


  • Prioritizing genetic variants
    • Non-synonymous variants (SIFT, PolyPhen)
    • Synonymous variants
    • Regulatory variants
  • Statistical methods on rare variants


Oct 4

RNA-seq I

  • Biological theories on RNA-seq experiments
  • Experimental considerations
  • Published examples
  • Major scientific advance using RNA-seq
  • Alignment
  • Gene expression analysis


Oct 11

Guest lecture - Dr. Sarath Janga 

  • Cloud computing  

RNA-seq II

  • Differential expression analysis
  • Alternative splicing


Oct 18


  • Transcript variation
  • Allele-specific expression
  • RNA editing
  • Non-coding RNA
  • Pair-ends/mate pairs - identify gene fusion
  • smRNA


Oct 25

ChIP-seq I

  • Biological theories on ChIP-seq analysis
  • Published studies
  • Experimental considerations
  • DNA frament evaluation
  • Peak identification
  • Two condition comparison
  • Saturation analysis


Nov 1

Guest lecture - Dr. Milan Radovich 

  • Next generation sequencing in cancer research 

Guest lecture - Dr. Matteo Vatta 

  • Clinical sequencing 


Nov 8

ChIP-seq II - Bioinformatics topics in ChIP-seq analysis

  • Motif finding and related theories
  • Integrate transcription factor binding data with RNA-seq experiment
  • Identify miRNA promoters using ChIP-seq data
  • Genetic variation in ChIP-seq-identified regions
  • RNA binding protein data analysis


Nov 15

ChIP-seq III: Epigenetics

  • DNA methylation
    • Experimental considerations
    • Statistical considerations
    • Bioinformatics tools
  • Histone modification
    • Experimental approaches
    • Statistical considerations
    • Hidden Markov model annotating histone marks


Nov 22

Student presentation


Nov 29

Thanksgiviing recess


Dec 6

final exam