Introduction to NGS Analysis

November 24-25, 2020

Lecturers: Vladimir Teif and Antonio Marco

 

This course that will teach you the basics of analysis of ChIP-seq and RNA-seq using an online platform Galaxy. For graduate students of the University of Essex, registration fees can be paid from the Proficio funding. 

Register here to obtain Zoom link

  

 

Schedule

24 Nov 2020

12:00 – 14:00

Virtual meeting

LECTURES: Intro & ChIP-seq

  1. Introduction to NGS methods | slides | recorded video
  2. NGS applications and basic data analysis | slides | recorded video

14:00 – 14:30

home

LUNCH BREAK

Lecturers will be available for Q&A and discussion of your research projects

14:30 – 17:00

Virtual meeting

PRACTICAL SESSION: ChIP-seq

Detailed instructions | recorded video

Practical plan

  1. Understand where to get NGS data online
  2. Familiarise yourself with Galaxy – an online platform for NGS analysis
  3. Learn about ChIP-seq data formats
  4. Use Bowtie2 in Galaxy to map reads reported by Younger et al. (2015).
  5. Find peaks of p53 ChIP-seq (p53 binding sites) using MACS2 in Galaxy
  6. Compare the peaks that we determined with the peaks reported by Younger et al.
  7. Intersect p53 peaks with enhancers and promoters using BedTools in Galaxy
  8. Fisher’s statistical test for enrichment analysis
  9. Heatmap visualisaiton with DeepTools in Galaxy
  10. Motif analysis with MEME

17.00 – 18:00

Virtual meeting

LECTURE: RNA-seq 1

Measuring gene expression | slides | recorded video

25 Nov 2020

12:00 – 12:30

Virtual meeting

LECTURE: RNA-seq 2

Differential gene expression | slides | recorded video (includes lecture and practical)

12:30 – 13:00

home

LUNCH BREAK

Lecturers will be available for Q&A and discussion of your research projects

13:00 – 14:30

Virtual meeting

PRACTICAL SESSION: RNA-seq

Practical plan (Please see detailed instructions in this document)

1. Understand RNAseq raw data format

2. Evaluate quality of RNAseq sequences (FastQC)

3. Map RNAseq reads to genomic sequences (TopHat)

4. Quantify the expression level of genes from RNAseq data (HTSeq)

5. Differential Gene Expression Analysis (DESeq2)

14:30 – 15:00

home

VIRTUAL COFFEE

You can take a break; lecturers will be available for Q&A

15:00 – 16:00

Virtual meeting

LECTURE: Integrative analysis

Integrating ChIP-seq and RNA-seq data | Slides | Video recording

16:00 – 16:30

Virtual meeting

BREAK + ROUND TABLE DISCUSSION

You can take a break; lecturers will be available for Q&A

16.30 – 18:00

Virtual meeting

PRACTICAL SESSION: Integrative Analysis

Detailed practical instructions are in this document | Video recording

  1. Integrating ChIP-seq and RNA-seq data
  2. Gene Ontology analysis with DAVID, EnrichR, GOrilla
  3. Network construction with PathwayCommons