Course Identification

Bioinformatics analysis of Next Generation Sequence (NGS) data
20193091

Lecturers and Teaching Assistants

Dr. Ester Feldmesser, Dr. Dena Leshkowitz, Dr. Tsviya Olender, Dr. Hadas Keren-Shaul, Dr. Ron Rotkopf, Dr. Bareket Dassa, Dr. Noa Wigoda
N/A

Course Schedule and Location

2019
First Semester
Thursday, 09:15 - 12:00, FGS, Rm B
08/11/2018

Field of Study, Course Type and Credit Points

Life Sciences: Lecture; Elective; 3.00 points
Life Sciences (Molecular and Cellular Neuroscience Track): Lecture; Elective; 3.00 points
Life Sciences (Brain Sciences: Systems, Computational and Cognitive Neuroscience Track): Lecture; Elective; 3.00 points
Life Sciences (Computational and Systems Biology Track): Lecture; Elective; 3.00 points

Comments

For second year MSc and forward. Not for first year MSc students.

Prerequisites

No

Restrictions

32

Language of Instruction

English

Registration by

30/10/2018

Attendance and participation

Required in at least 80% of the lectures

Grade Type

Numerical (out of 100)

Grade Breakdown (in %)

20%
40%
40%

Evaluation Type

Examination

Scheduled date 1

07/03/2019
FGS, Rm C
1000-1200
N/A

Scheduled date 2

19/03/2019
FGS, Rm B
1000-1200
N/A

Estimated Weekly Independent Workload (in hours)

2

Syllabus

  1. Introduction to Illumina  NGS technology
  2. NGS applications and introduction to analysis
  3. Illumina Primary Analysis Pipeline & Quality Control
  4. Sequence alignment to genome
  5. RNA-Seq gene level differential expression and Mars-seq analysis
  6. RNA-Seq transcript level analysis and de novo transcriptome assembly
  7. Clustering analysis on gene expression data
  8. Functional analysis: Gene Ontology and pathways
  9. Single cell RNA-Seq
  10. Variant detection
  11. Additional genomic technologies: PacBio and 10xGenomics
  12. In-house developed NGS pipelines interface

Learning Outcomes

Upon successful completion of the course students will be able to:

  1. Demonstrate familiarity with the common applications of deep-sequencing.
  2. Discuss the basics steps of data analysis.
  3. Extract the biological meaning of the results.

Reading List

  1. Brown, S. M. Next-generation DNA sequencing informatics: . 2nd ed. Cold Spring Harbor Laboratory Press.
  2. Next-generation genomics: an integrative approach R. David Hawkins, Gary C. Hon & Bing Ren Nature Reviews Genetics 11, 476-486 (July 2010) | doi:10.1038/nrg2795
  3. http://www.nature.com/subjects/next-generation-sequencing

Website

N/A