Course Identification

Title:

An Introduction to deep-sequencing data analysis

Code:

20183312

Lecturers and Teaching Assistants

Lecturers:

Dr. Ester Feldmesser, Dr. Dena Leshkowitz, Dr. Tsviya Olender, Dr. Hadas Keren-Shaul, Dr. Ron Rotkopf, Dr. Gil Stelzer

TA's:

N/A

Course Schedule and Location

Year:

2018

Semester:

Second Semester

When / Where:

17-27/6, 9:00-13:30, FGS, Rm B

First Lecture:

17/06/2018

End date:

27/06/2018

Field of Study, Course Type and Credit Points

Life Sciences: Laboratory; Elective; 1.00 points
Life Sciences (Systems Biology Track): 1.00 points
Life Sciences (Molecular and Cellular Neuroscience Track): 1.00 points

Comments

It is recommended that people that are not familiar with Linux will participate in an introductory workshop. The date and venue of the workshop will be announced later.
The course will include a final assignment in which the students can analyse their own NGS data upon approval.

Prerequisites

No

Restrictions

Participants:

32

Language of Instruction

English

Registration by

Registration By:16/04/2018

Attendance and participation

Obligatory

Grade Type

Pass / Fail

Grade Breakdown (in %)

Attendance

50%

Final:

50%

Evaluation Type

Laboratory

Scheduled date 1

Date / due date

N/A

Location

N/A

Time

-

Remarks

N/A

Estimated Weekly Independent Workload (in hours)

5

Syllabus

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

Learning Outcomes

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

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

Reading List

Brown, S. M. Next-generation DNA sequencing informatics: . 2nd ed. Cold Spring Harbor Laboratory Press.
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
http://www.nature.com/subjects/next-generation-sequencing

Website

N/A