wiki

Welcome to the Helmholtz Summer School on Chromatin Biology: A hands-on expedition

Tutorials

• UNIX shell commands
  • UNIX Tutorial for Beginners
  • Introduction to the Command Line for Genomics
  • cheat sheet
  • for Windows users: MobaXterm client
• R/Rstudio/Bioconductor
  • Intro to R and RStudio for Genomics
• IGV Browser

Installations

• Install R (version R-4.2.1)
• Install RStudio (version RStudio-2022.07.0)
• Install required packages
  • Bioconductor (version 3.15)

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.15")

BiocManager::install(c("ChIPseeker", "GenomicRanges", "rtracklayer", "TxDb.Hsapiens.UCSC.hg19.knownGene", "clusterProfiler","AnnotationHub"))

Preliminary Schedule

Wednesday

• 09:00 Introduction

  • Reproducible Research
  • Introduction to SLURM and HPC

• 11:00 Workflow management

  • Snakemake tutorial
  • Workflow explained step-by-step
  • Snakemake Workflow

• 13:00 Lunch

• 14:00 External seminar

• 15:00 Data processing I

  • Quality Control (FastQC, multiQC)
  • Alignment (Bowtie2)
  • File formats (fasta, fastq, bam)

Thursday

• 9:00 Data processing II

  • Genome coverage (Deeptools)
  • Peak finding (MACS2)
  • File formats (bed, bedgraph)
  • IGV session

• 10:30 Run Pipeline

• 11:00 IGV session

  • bigwig
  • peaks

• 12:00 Correlation analysis

• Bonus

  • Basic Dataviz with Deeptools

    • profile plot
    • heatmap

  • Motif Search

    • consensus peaks with bedtools
    • find motifs with Homer

  • Snakemake final exercise

    • implement Deeptools profile plot in Snakemake

• 13:00 Lunch

• 14:00 External seminar

• 15:00 Working with peaks in R
  We gonna use the course data for downstream analysis.

  • Introduction to R, Rmarkdown and Bioconductor
  • Import MACS peak files into R and filtering
  • GenomicRanges
  • ENCODE blacklisted regions and how to remove them
  • Handling multiple BED file with GRangesLists
  • Consensus peak sets, reproducible peaks and peak unions
  • Visualizing peak subsets/overlaps (UpSetR, VennDiagram, eulerr)

Friday

• 09:00 Working with peaks in R continued

  • A short introduction into ggplot2
  • Peak annotation and comparison (ChIPpeakanno, ChIPseeker)
  • Inferring biological meaning with over-representation analysis (ClusterProfiler)

• 12:00 Lunch

• 13:00 Workflow results

  • Looking at actual workflow output folder
  • Review of MultiQC report
  • Comparison of samples with different quality

• 14:00 External seminar

• 15:00 Q&A

  • Final bioinformatics discussion

• 16:00 General course feed back