An Introduction to deep-sequencing analysis for biologists 2019 - 2020
Course requirements			Exercise final grades
Date	Time	Location	Topic	Lecturers
Nov 5th	09:15-11:00	Wolfson lectures hall	Next Generation Sequencing (NGS) what and why (Gil), (Noa)	Gil Stelzer and Noa Wigoda
Nov 6th	11:15-12:00	Feinberg computers room B	Exercise 1 (Due Nov. 12) mount info mount_clean.bat	Gil Stelzer and Noa Wigoda
			Exercise 1: Grades

Nov 12th	09:15-10:00	Wolfson lectures hall	Introduction to Illumina NGS technology Lecutre postponed	Ester Feldmesser
	10:15-11:00		Illumina primary analysis Lecture postponed	Noa Wigoda

Nov 19th	09:15-10:00	Wolfson lectures hall	Introduction to Illumina NGS technology	Ester Feldmesser
	10:15-11:00		Illumina Primary Analysis & Quality Control	Noa Wigoda
Nov 20th	11:15-12:00	Feinberg computers room B	Exercise 2 (Due Nov. 26) FastQC reports exp_73 exp_16	Gil Stelzer and Noa Wigoda
			Exercise 2 recitation Exercise 2: Grades

Nov 26th	09:15-10:00	Wolfson lectures hall	Sequence alignment or mapping	Ester Feldmesser
	10:15-11:00		Alignment visualization	Ester Feldmesser
Nov 27th	11:15-12:00	Feinberg computers room B	Exercise 3: (Due Dec. 3)	Ester Feldmesser and Noa Wigoda
			Exercise 3: Grades

Dec. 3rd	09:15-11:00	Wolfson lectures hall	Gene Expression Analysis (RNA-seq & MARS-seq)	Dena Leshkowitz
Dec. 4th	11:15-12:00	Feinberg computers room B	Exercise 4: UTAP: User-friendly Transcriptome Analysis Pipeline (Due Dec. 10)	Dena Leshkowitz and Bareket Dassa
			Exercise 4: Grades

Dec. 10th	9:15-11:00	Wolfson lectures hall	Clustering and Exploratory Analysis	Ester Feldmesser
			Exercise 5 (Due Dec. 24)	Ester Feldmesser

Dec 17th	09:15-10:00	Wolfson lectures hall	Functional analysis: Gene Ontology	Noa Wigoda
	10:15-11:00		Functional analysis: Pathways analysis	Bareket Dassa
Dec. 18th	11:15-12:00	Feinberg computers room B	Exercise 5 (Due Dec. 24)	Ester Feldmesser and Bareket Dassa
			Exercise 5: Grades
Dec 18th	11:15-12:00	Feinberg computers room B	Exercise 6: Functional analysis, EXCEL_tips (Due Dec. 24)	Noa Wigoda and Bareket Dassa
			Deseq_all_results.txt, Kmeans_ex6.csv, arabidopsis_rld.csv
			Exercise 6: Grades

Dec 24th	09:15-10:00	Wolfson lectures hall	Assembly and quantification of transcripts from RNA-Seq data	Dena Leshkowitz
	10:15-11:00		Third Generation sequencing tecnologies: PacBio SMRT and Nanopore	Gil Stelzer
Dec 25th	No Class		Exercise 7: IGV comparing algorithms and platforms (Due Dec. 31)	Dena Leshkowitz and Gil Stelzer
			Exercise 7: Grades

Dec 31st	09:15-11:00	Wolfson lectures hall	Variant detection	Tsviya Olender
Jan 1st	11:15-12:00	Feinberg computers room B	Exercise 8: Variant detection (Due Jan. 7)	Tsviya Olender and Bareket Dassa
			Exercise 8: Grades

Jan 7th	09:15-10:00	Wolfson lectures hall	ChIP-Seq: Using NGS to Discover Protein-DNA Interactions	Dena Leshkowitz
	10:15-11:00		ATAC-seq	Bareket Dassa
Jan 8th	11:15-12:00	Feinberg computers room B	Exercise 9 (Due Jan. 14)	Dena Leshkowitz, Noa Wigoda and Bareket Dassa
			Exercise 9: Grades

Jan 14th	09:15-10:00	Wolfson lectures hall	Dimensionality Reduction	Ron Rotkopf
Jan 14th	09:15-10:00	Wolfson lectures hall	Introduction to Single-cell RNA-sequencing (scRNA-seq) Analysis	Dena Leshkowitz
	10:15-11:00		Single cell analysis, Seurat	Gil Stelzer
Jan 15th	11:15-12:00	Feinberg computers room B	Exercise10: Single cell RNA-seq Analysis (Due Jan. 21)	Dena Leshkowitz and Gil Stelzer
			Exercise 10: Grades

Jan 21st	09:15-10:00	Wolfson lectures hall	Metagenomics	Bareket Dassa
	10:15-11:00		Course summary + Q&A	Dena Leshkowitz
Jan 22th	11:15-12:00	No Exercise

Jan 28th	09:15-11:00	Wolfson lecture hall	Example questions for the exam Answers for the exam example questions Illumina Sequencing additional remarks Students Questions -Preparing for exam

Feb 13th	10:00-12:00	Wolfson lecture hall	Exam Schedule A
Mar 19th	10:00-12:00	Wolfson lecture hall	Exam Schedule B

An Introduction to deep-sequencing analysis for biologists 2019 - 2020

Course requirements

Exercise final grades