Bioinformatics Group

Institute of Molecular Biology NAS RA

Courses

Course: Bioinformatics and Functional Genomics

 

A hybrid course consisting of intro to Next Generation Sequencing technologies and continuing with the EdX course: Case studies in Functional Genomics

The next months will be dedicated to learning the nature of data produced by Next Generation Sequencing (NGS) technologies and their applications, with practical sessions to perform functional genomics studies. The first part will be conducted based on selected papers in functional genomics and will then continue with the EdX course “Case studies in functional genomics”. We will self-audit this course before the meetings and will discuss the lectures and the exercises during the meeting. Please, review the materials beforehand, in order to have an effective discussion later on.

 

Next session: 23 November, Thursday, at 18:00-19:30. 

Part 3. Variant calling: theory and practice

Previous session (16 November, Thursday):  Variant calling: theory and practice


Program

Part 1. Intro to NGS technologies: data generation and quality control

Materials:


Date: 26 October, Thursday, 17:30-19:30


History and classification of sequencing technologies: 


Paper 1: The sequence of sequencers: The history of sequencing DNA


Paper 2: Ten years of next-generation sequencing technology


Slides Oct26: Intro to NGS technologies


 


Date: 02 November, Thursday, 17:30-19:30


Quality control of data from Illumina sequencers 


The programs that read the image files from sequencers and convert those to sequences, along with reporting quality scores, are called base callers. The quality of base calling depends on multiple factors. We will discuss those factors shortly.


Additionally, we will discuss the following paper about various quality score formats:


Paper 3: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants


We will next discuss the FASTQC program to analyze quality of the reads.


Please, watch this video tutorial on FASTQC.


The following is the documentation of FASTQC. Please, look at the documentation in parallel with the two examples of fastqc outputs: for good and for bad Illumina data.


Slides Nov02: Quality control



Part 2. Short read alignment


Date: 09 November, Thursday, 18:00-19:30


We will start the meeting with pairwise sequence alignment algorithm. Please, have a look at the chapter from the start till 2.1.2 Local alignment.


We’ll then discuss the first successful attempt of fast short-read alignment:


Paper 4: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (bowtie).


As well as the adaptation of the method to map RNA-seq reads:


Paper 5: TopHat: discovering splice junctions with RNA-Seq. 


Slides Nov09: Alignment


 



Part 3. Variant calling: theory and practice


Date: 16 November, Thursday, 18:00-19:30


What is paired-end sequencing? We will review the pros and cons of this technology and the specifics of paired-end read mapping.


Please watch the following presentation Paired end and Mate pair Sequencing: What is it and How is it done?


We will then discuss the concept of variant calling and how it is performed.


Finally, the Sequence Alignment/Map(SAM) format will be discussed. Please have a look at SAM format specifications.


Date: 23 November, Thursday, 18:00-19:30


We will start our meeting with a discussion of​ variant calling tool HaplotypeCaller from Genome Analysis Toolkit (GATK). Please, have a look at variant calling tutorial.


Then we will ​have some practice with HaplotypeCaller. Please, try to use it and run the codes. In tutorials folder you can find the data used in the tutorial.


Finally, we’ll get an idea of SAM format specifications.



Part 4. EdX course: RNA-Seq

Materials: see EdX instructions


Dates:


Part 5. New algorithms in RNA-Seq analysis: pseudoalignment

Materials: TBD


Dates:


Part 6. EdX course: ChIP-Seq

Materials: see EdX instructions


Dates:


Part 7. EdX course: Bisulfite-Seq

Materials: see EdX instructions


Dates:

 


When and where

Where: The courses will be held at BIG, in the the Institute of Molecular Biology, on the 3rd Floor. Turn left from the elevator, find our sign on one of the doors on the right side of the corridor and enter.

When: Each Thursday, from 17:30 – 19:30. First session: 26 October.

 


How to join

The course is open for everyone. If you’d like to join, please, let us know by:

  • emailing us at big@sci.am,
  • calling +37494601703 (Lilit),
  • writing a message to our FB page

fb

Join our Facebook group to get involved in online discussions.

 

 

 


EdX instructions

To register: If you don’t have an edX account, you should create one at https://courses.edx.org/login.

After registration: If you have an account you should sing in. Then proceed to the course page and hit the “Enroll now” button at the top right. A new page will ask you if you’d like to receive a certificate for the course (not free). We assume that you won’t, so scroll down and hit the free “Audit This Course” button.

Congratulations! You are now enrolled in the course.

After enrollment: Proceed to the course page and click the “Open Course” button. Keep patience, you will hit the “Resume course” button in the next page and you’re done!

After opening the course: You will see the course schedule on the left sidebar. Watch the introductory videos to get familiar with the course and start auditing the course. Follow each weeks agenda to know which week’s materials to view. You should also solve the problems in the “exercises” section so that we discuss them later.