Introduction to NGS Analysis
November 24-25, 2020
Lecturers: Vladimir Teif and Antonio Marco
This course 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.
Schedule
24 Nov 2020
12:00 – 14:00
Virtual meeting
LECTURES: Intro & ChIP-seq
- Introduction to NGS methods | slides | recorded video
- 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
- Understand where to get NGS data online
- Familiarise yourself with Galaxy – an online platform for NGS analysis
- Learn about ChIP-seq data formats
- Use Bowtie2 in Galaxy to map reads reported by Younger et al. (2015).
- Find peaks of p53 ChIP-seq (p53 binding sites) using MACS2 in Galaxy
- Compare the peaks that we determined with the peaks reported by Younger et al.
- Intersect p53 peaks with enhancers and promoters using BedTools in Galaxy
- Fisher’s statistical test for enrichment analysis
- Heatmap visualisaiton with DeepTools in Galaxy
- 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
- Integrating ChIP-seq and RNA-seq data
- Gene Ontology analysis with DAVID, EnrichR, GOrilla
- Network construction with PathwayCommons