Introduction to Deep Sequencing Analysis course 2017

Date

Hours

Subject

Lecturer

June 4th

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

11:45-12:30

Exercise 1: Introduction to Linux & WEXAC cluster

Dena Leshkowitz & Esti Feldmesser

June 5th

09:00-10:00

Illumina primary analysis pipeline & sequence quality control

Dena Leshkowitz

10:15-11:00

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 6th

09:00-10:15

Gene expression analysis of RNA-Seq data

Dena Leshkowitz

10:30-11:00

Exercise 3 : Analyzing RNA-Seq data

Dena Leshkowitz & Esti Feldmesser

11:15-12:00

Introduction to R & Bioconductor

Ron Rotkopf

12:00-12:30

Exercise 4: Introduction to R

Ron Rotkopf

June 7th

09:00-09:45

Clustering

Esti Feldmesser

10:00-11:30

Exercise 5: Learn how to detect and cluster differentially expressed genes from RNA-Seq data using DESeq2

Dena Leshkowitz & Esti Feldmesser

11:45-12:30

Single Cell RNA-Seq & 10X Genomics technology

Hadas Keren-Shaul

June 8th

09:00-09:45

Assembly and quantification of transcripts from RNA-Seq data

Dena Leshkowitz

10:00-10:30

Analysing RNA-Seq data produced by Mars-Seq protocol

Dena Leshkowitz

10:45-11:15

Exercise 6: Analysing transcript assembly of RNA-Seq data

Dena Leshkowitz & Esti Feldmesser

11:30-12:30

Start final exercise

All instructors

June 11th

09:00-10:00

Functional analysis: Gene Ontology and pathways

Ester Feldmesser

10:15-11:00

Demo: Ingenuity, Exercise 7: GSEA

Esti Feldmesser

11:15-12:30

Variant detection

Tsviya Olender

June 12th

09:00-10:30

Exercise 8: Variant detection

Tsviya Olender & Dena Leshkowitz

10:45-11:30

ChIP-Seq: Using NGS to Discover Protein-DNA Interactions

Dena Leshkowitz

11:45-12:30

Exercise 9: Analyzing ChIP-Seq data

Dena Leshkowitz & Esti Feldmesser

June 13th

09:00-09:45

Exercise 10: Functional Analysis for animals and plants

Dena Leshkowitz & Esti Feldmesser

10:00-12:30

Final Exercise

All instructors

June 14th

09:00-10:00

Final Exercise

All instructors

10:00-10:30

RNA-Seq Pipeline Interface

Refael Kohen

10:45-11:15

PacBio SMRT sequencing technology

Hadas Keren-Shaul

11:15-11:45

Analysis of PacBio sequence data

Ester Feldmesser

11:45-12:30

Course Summary: Questions & Answers

Dena Leshkowitz