Introduction to Deep Sequencing Analysis course 2018

Date

Time

Topic

Lecturer

June 17th

09:00-10:30

Introduction to Illumina NGS technology, library preparations and Mars-seq

Hadas Keren-Shaul

10:45-11:30

NGS applications and introduction to analysis

Esti Feldmesser

11:45-13:00

Exercise 1: Introduction to Linux & WEXAC cluster

Dena Leshkowitz & Esti Feldmesser

June 18th

09:00-09:50

Illumina primary analysis pipeline & sequence quality control

Dena Leshkowitz

10:00-10:45

Sequence alignment to genome (bowtie, tophat, star, bwa)

Ester Feldmesser

11:15-12:30

Exercise 2: Using WEXAC for mapping and sequence QC

Dena Leshkowitz & Esti Feldmesser

June 19th

09:00-10:00

Gene expression analysis of RNA-Seq data

Dena Leshkowitz

10:15-11:00

Exercise 3 : Analyzing RNA-Seq data

Dena Leshkowitz & Esti Feldmesser

11:15-12:00

Introduction to R & Bioconductor

Ron Rotkopf

12:15-13:00

Exercise 4: Introduction to R

Ron Rotkopf

June 20th

09:00-10:00

Clustering

Esti Feldmesser

10:15-12:00

Exercise 5: Learn how to detect and cluster differentially expressed genes from RNA-Seq

Dena Leshkowitz & Esti Feldmesser

12:15-13:00

Analysing RNA-Seq data produced by Mars-Seq protocol

Dena Leshkowitz

June 21st

9:00-9:45

UTAP NGS Pipeline Interface

Dena Leshkowitz

10:00-10:45

Assembly and quantification of transcripts from RNA-Seq data

Dena Leshkowitz

11:00-11:45

Exercise 6: Analysing transcript assembly of RNA-Seq data

Dena Leshkowitz & Ester Feldmesser

12:00-12:45

Single Cell RNA-Seq & 10X Genomics technology

Hadas Keren-Shaul

June 24th

09:00-10:00

Functional analysis: Gene Ontology and pathways

Ester Feldmesser

10:15-11:00

The GeneCards suite

Gil Stelzer

11:00-11:30

Gene Set Enrichment Analysis

Ester Feldmesser

11:30-13:00

Exercise 7: Functional Analysis for animals and plants: MINE & Revigo, GSEA

Ester Feldmesser & Gil Stelzer

June 25th

09:00-10:30

Variant detection

Tsviya Olender

10:45-11:45

Exercise 8: Variant detection

Tsviya Olender & Dena Leshkowitz

12:00-13:00

Final Exercise

All instructors

June 26th

09:00-09:45

Single cell RNA-seq

Dena Leshkowitz

10:00-10:45

Exercise 9: Single cell RNA-seq

Dena Leshkowitz & Gil Stelzer

11:00-13:00

Final Exercise

All instructors

June 27th

09:00-10:30

Final Exercise

All instructors

10:45-11:15

PacBio SMRT sequencing technology

Hadas Keren-Shaul

11:15-11:45

Nanopore

Hadas Keren-Shaul

11:45-12:30

Course Summary: Questions & Answers

Dena Leshkowitz