Bar Ilan University Faculty of Medicine

Next Generation Sequencing bioinformatics

81-948, 2013

Instructor: Dr. Eli . Reuveni et biu dot ac dot il

Description | Schedule | Coursework | Students | Bibliography

Description

The course aims for graduate students and post-doctoral researchers who need to apply next generation sequencing (NGS) technologies and bioinformatics methods in their research. The course covers both theoretical lectures and practical sessions. The main goal of the course is to give a solid background and experience with next generation sequencing, analyzing ChIP-Seq and RNA-Seq datasets. Lectures cover the following topics: quality assessment and visualisation of RNA-Seq and ChIP-Seq data, differential expression of ChIP and RNA-Seq data, integration with external databases, as well as variant detection. Practical sessions of the course consist of computer exercises that will enable the participants to apply data analysis tools using Linux as well as an introduction to statistical methods relevant for deep sequencing analysis.

 

The course meets on Tuesdays at 11:00 – 16:00 in room 102 building B of the Faculty of Medicine.

Schedule

Date

Time

Topic

 

 

TUE 13/5

11:00 – 11:45

11:45 – 12:15

12:15 – 12:45

12:45 – 13:00

13:00 – 13:45

13:45 – 14:00

14:15 – 15:00

Introduction to NGS (lecture)

NGS introduction (exercise)

Break

Introduction to Linux environment (lecture)

NGS quality control and intro to common NGS files (lecture)

Break

NGS quality control and intro to common NGS files (practical)

 

 

TUE 20/5

11:00 – 11:45

11:45 – 12:15

12:15 – 12:45

12:45 – 13:45

13:45 – 14:00

14:00 – 15:00

Introduction to ChIP-seq (lecture)

ChIP-seq analysis: alignment and visualization  (practical)

Break

ChIP-seq analysis: alignment and visualization  (practical)

Break

ChIP-seq analysis: peak identification and motif discovery (practical)

 

 

TUE 27/5

11:00 – 11:45

11:45 – 12:15

12:15 – 12:45

12:45 – 13:45

13:45 – 14:00

14:00 – 15:00

Introduction to RNA-seq (lecture)

RNA-seq: alignment (practical)

Break

RNA-seq: transcriptome assembly (practical)

Break

RNA-seq: Differential expression (practical)

 

 

TUE 10/6

11:00 – 11:45

11:45 – 12:15

12:15 – 12:45

12:45 – 13:45

13:45 – 14:00

14:00 – 15:00

Introduction to genome variation (lecture)

Genome variation: mapping (practical)

Break

Genome variation: SNP calling (practical)

Break

Genome variation: SNP functional annotation (practical)

 

Coursework 

Bibliography

·         Trapnell C, Pachter L, Salzberg SL. Bioinformatics. 2009 May 1;25(9):1105-11

 

·         Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L.

Differential analysis of gene regulation at transcript resolution with RNA-seq.

Nat Biotechnol. 2013 Jan;31(1):46-53

 

·         Feng J, Liu T, Qin B, Zhang Y, Liu XS. Identifying ChIP-seq enrichment using

MACS. Nat Protoc. 2012 Sep;7(9):1728-40

 

·         McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303