Introduction to Deep Sequencing Analysis course 2018 - 2019
Course requirements and grades
Date	Time	Topic	Lecturer
Nov 8th	09:15-10:30	Introduction to Illumina NGS technology, library preparations and Mars-seq	Hadas Keren-Shaul
	10:45-12:00	Introduction to Linux & WEXAC cluster	Esti Feldmesser

Nov 15th	09:15-10:00	Exercise 1: Introduction to Linux & WEXAC cluster	Ester Feldmesser, Bareket Dassa and Noa Wigoda
	10:15-11:00	What can we do with NGS data?	Ester Feldmesser
	11:15-12:00	Illumina primary analysis pipeline & sequence quality control	Dena Leshkowitz
		Due Nov 19th: Exercise 1 Linux
		Exercise 1: Answers

Nov 22th	09:15-10:00	Sequence alignment to genome (bowtie, tophat, star, bwa)	Ester Feldmesser
	10:15-11:00	Running mapping commands and viewing the results	Esti Feldmesser
	11:00-12:00	Exercise 2: Using WEXAC for mapping and sequence QC	Dena Leshkowitz & Ester Feldmesser and Noa Wigoda
		Due Nov 26th: Exercise 2, Answers

Nov 29th	09:15-10:30	Gene expression analysis of RNA-Seq data	Dena Leshkowitz
	10:40-12:00	Exercise 3: Analyzing RNA-Seq data	Dena Leshkowitz, Ester Feldmesser and Bareket Dassa
		Due Dec 3rd: Exercise 3, Answers

Dec 6th	9:15-10:00	Clustering	Ester Feldmesser
	10:15-11:00	Introduction to R & Bioconductor	Ron Rotkopf
	11:15-12:00	Exercise 4: Introduction to R	Ron Rotkopf

Dec 13th	09:15-12:00	Exercise 5: Learn how to detect and cluster differentially expressed genes from RNA-Seq data using DESeq2	Dena Leshkowitz, Ester Feldmesser, Bareket Dassa and Noa Wigoda
		Due Dec 24th: Exercise 5, Answers

Dec 20th	09:15-9:45	Analysing Bulk Mars-Seq data	Dena Leshkowitz
	9:45-10:15	UTAP: Transcriptome Pipelines Interface	Dena Leshkowitz
	10:30-12:00	Functional analysis: Gene Ontology and pathways	Ester Feldmesser

Dec 27th	09:15-10:00	Functional analysis: Gene Set Enrichment (GSEA)	Ester Feldmesser
	10:15-11:00	GeneAnalytics	Bareket Dassa
	10:15-12:00	Exercise 6: Functional Analysis for animals and plants GeneAnalytics, GSEA and MINE & Revigo	Ester Feldmesser and Bareket Dassa
		Due Jan 3rd: Exercise 6, Answers

Jan 3rd	09:15-10:00	Assembly and quantification of transcripts from RNA-Seq data	Dena Leshkowitz
	10:15-12:00	Exercise 7: Analysing transcript assembly of RNA-Seq data	Dena Leshkowitz, Noa Wigoda, Bareket Dassa and Ester Feldmesser
		Due Jan 7th: Exercise 7, Answers

Jan 10th	09:15-10:30	Variant detection	Tsviya Olender
	10:45-12:00	Exercise 8: Variant detection	Tsviya Olender and Dena Leshkowitz
		Due Jan 14th: Exercise 8, Answers

Jan 17th	09:15-10:00	ChIP-Seq: Using NGS to Discover Protein-DNA Interactions	Dena Leshkowitz
	10:15-11:00	Exercise 9: Analyzing ChIP-Seq data	Dena Leshkowitz and Noa Wigoda
	11:15-12:00	Tips Excel, Help in Exercises	Dena Leshkowitz, Noa Wigoda and Bareket Dassa
		Due Jan 28st: Exercise 9, Answers

Jan 24th	09:15-10:00	ATAC-Seq	Bareket Dassa
	10:15-11:00	Single Cell RNA-Seq & 10X Genomics technology	Hadas Keren-Shaul
	11:15-12:00	Introduction to Single cell RNA-seq Analysis	Dena Leshkowitz


Jan 31st	09:15-10:15	Third Generation sequencing tecnologies: PacBio SMRT and Nanopore	Hadas Keren-Shaul
	10:30-12:00	Summary Exercise	Dena Leshkowitz, Bareket Dassa and Ester Feldmesser

Feb 7th	09:15-12:00	Students Questions -Preparing for exam and Summary exercise	Dena Leshkowitz, Noa Wigoda and Ester Feldmesser
		Example questions for the exam