An Introduction to deep-sequencing analysis for biologists 2021 - 2022

Click here for the course requirements

Date

Time

Location

Topic

Lecturers

25-Oct

10:15-12:00

Feinberg room C

Experimental design

Noa Wigoda

28-Oct

9:15-10:00

Feinberg computers room B

Exercise 1: Experimental design (Due 4.11.21) Exercise 1: answers

Noa Wigoda

Nov 1st

10:15-12:00

Feinberg room C

Introduction to Illumina NGS technology

Ester Feldmesser

Nov 8th

10:15-12:00

Feinberg room C

Illumina primary analysis

Noa Wigoda

Nov 11th

9:15-10:00

Feinberg computers room B

Exercise 2: Quality control (FastQC) is in the Moodle (Due 18.11.21)

Noa Wigoda, Gil Stelzer

Nov 15th

10:15-11:00

Feinberg room C

Sequence alignment or mapping

Ester Feldmesser

11:15-12:00

Alignment visualization

Ester Feldmesser

Nov 18th

9:15-10:00

Feinberg computers room B

Exercise 3: IGV, looking at bam files is in the Moodle (Due 25.11.21) Exercise 3: answers

Ester Feldmesser

Nov. 22nd

10:15-12:00

Feinberg room C

Gene Expression Analysis (RNA-seq & MARS-seq)

Dena Leshkowitz

Nov. 25th

9:15-10:00

Feinberg computers room B

Exercise 4: UTAP: User-friendlyTranscriptome Analysis
Pipeline, eLearning- is in the Moodle (Due 6.12.21)

Dena Leshkowitz, Bareket Dassa

Nov. 29th

10:15-11:00

Feinberg room C

Clustering

Ester Feldmesser

11:15-12:00

Exploratory analysis

Ester Feldmesser

Dec 2nd

9:15-10:00

Feinberg computers room B

Demonstration of clustering with Partek

Ester Feldmesser

Dec 6th

10:15-11:00

Feinberg room C

Functional analysis: Gene Ontology

Noa Wigoda

11:15-12:00

Functional analysis: Pathways analysis

Bareket Dassa

Dec. 9th

9:15-10:00

Feinberg computers room B

Exercise 5: gProfiler and Gene Analytics - is in the Moodle (Due 15.12.21)

Noa Wigoda, Bareket Dassa

Dec 13th

10:15-11:00

Feinberg room C

Assembly and quantification of transcripts from RNA-Seq data

Dena Leshkowitz

11:15-12:00

Long read sequencing using Oxford Nanopore Technology (ONT)
and Pacific Biosciences (PacBio)

Gil Stelzer

Dec 15th

9:15-10:00

Feinberg computers room B

Open Exercise

Ester Feldmesser

Dec 20th

10:15-12:00

Feinberg room C

Variant detection

Tsviya Olender

Dec 23th

9:15-10:00

Feinberg computers room B

Exercise 6: Variant detection (Due )

Tsviya Olender, Gil Stelzer

Dec 27th

10:15-11:00

Feinberg room C

ChIP-Seq: Using High-Throughput Sequencing to Discover
Protein-DNA Interactions

Dena Leshkowitz

11:15-12:00

ATAC-Seq: mapping chromatin accessibility

Bareket Dassa

Dec 30th 9:15-10:00 Feinberg computers room B Exercise 7: run ChIP/ATAC via UTAP pipelines (Due )

Dena Leshkowitz, Bareket Dassa

Jan 3rd

10:15-11:00

Feinberg room C

Introduction to Single-cell RNA-sequencing (scRNA-seq)

Gil Stelzer

11:15-12:00

scRNA analysis : From the Single Cell Count Matrix to Biological
Knowledge (using Seurat)

Dena Leshkowitz

Jan 6th 9:15-10:00 Feinberg computers room B Exercise 8: scRNA analysis (Due )

Dena Leshkowitz, Gil Stelzer

Jan 10th

10:15-11:00

Feinberg room C

Metagenomics

Bareket Dassa

Jan 17th

10:15-11:00

Feinberg room C

Course summary + Q&A

Jan 28th

10:15-12:00

Feinberg room C

Example questions for the exam

Feinberg room C

Exam Schedule A

Feinberg room C

Exam Schedule B