Introduction to Deep Sequencing Analysis course 2016

Date	Hours	Subject	Lecturer
March 13th	09:00-10.45	Introduction to Illumina NGS technology	Shmulik Motola
	11:00-12:00	NGS applications and introduction to analysis	Esti Feldmesser
	12:00-12:30	Lunch
	12:30-13:30	Illumina Primary analysis Pipeline and Quality Control, Sequence alignment to genome	Dena Leshkowitz & Esti Feldmesser
	13:30-14:30	Exercise 1: Chipster for QC and Mapping	Dena Leshkowitz & Esti Feldmesser

March 14th	09:00-10:15	Introduction to RNA-Seq analysis gene expression analysis (HTSeq, DESeq)	Dena Leshkowitz
		Introduction to RNA-Seq analysis VIDEO
	10:30-12:15	Exercise 2: Learn how to detect differentially expressed genes from RNA-Seq data with Chipster	Dena Leshkowitz & Naama Kopelman
	12:15-12:45	Lunch
	12:45-13:15	Clustering	Gilgi Friedlander
		Clustering VIDEO
	13:15-14:30	Exercise 3: Clustering	Gilgi Friedlander & Naama Kopelman

March 15th	09:00-10:00	RNA-Seq transcript level analysis	Dena Leshkowitz
	10:00-11:15	Exercise 4: Using Chipster for transcript assembly	Dena Leshkowitz & Esti Feldmesser
	11:30-13:00	Functional analysis: Gene Ontology and pathways	Esti Feldmesser
	13:00-13:30	Lunch
	13:30-14:30	Exercise 5: Functional analysis for animals and plants: David and ThaleMine, Tools table	Esti Feldmesser & Naama Kopelman

March 16th	09:00-10:00	Advanced functional analysis: Gene Set Analysis (GSEA) and Ingenuity; Exercise Input	Esti Feldmesser
		Advanced functional analysis VIDEO
	10:15-11:00	Demo: Ingenuity, Exercise 6: GSEA	Esti Feldmesser & Dena Leshkowitz
	11:15-12:30	ChIP-Seq: Using NGS to Discover Protein-DNA Interactions	Dena Leshkowitz
		ChIP-Seq: Using NGS VIDEO
	12:30-13:00	Lunch
	13:00-14:30	Exercise 7: ChIP-Seq Analysis	Dena Leshkowitz & Esti Feldmesser

March 17th	09:00-9:15	Starting Final Exercise	Esti Feldmesser
	09:15-10:30	Variant detection	Barak Markus
		Variant detection VIDEO
	10:45-12:00	Final Exercise	Esti Feldmesser & Dena Leshkowitz & Gilgi Friedlander
	12:00-12:30	Lunch
	12:30-13:30	Introduction to single-cell transcriptomics, Fluidigm platform for Single Cell Genomics	Esti Feldmesser & David Pilzer
		Single Cell Genomics VIDEO
	13:30-14:30	Course Summary: Questions & Answers	Dena Leshkowitz
		Course Summary: Questions & Answers VIDEO