/IntegratedATACseqAnalysisWorkshop2021

Primary LanguageROtherNOASSERTION

Integrated ATAC-seq Data Analysis Workshop: from Fastq to plots

Instructors name and contact information

Workshop description

ATAC-seq stands for Assay for Transposase-Accessible Chromatin using sequencing, which leverages a hyperactive transposase, namely Tn5, to cleave and tag ("tagmentation") double-strand DNA with sequencing adaptors at the same time. ATAC-seq is a faster yet more sensitive method for analyzing genome-wide chromatin accessibility. It is mostly used to determine if there are any changes regarding the open chromatin landscape between control and treatment group. For the demonstration session, this workshop focuses on the downstream post-alignment quality control analysis with the R package ATACseqQC.

Pre-requisites

  • General understanding of ATAC-seq analysis or have strong interests
  • Basic knowledge of R or Python
  • Familiar or have interests in the following concepts:
    • Peak calling/annotation
    • Nucleosome positioning
    • Transcription factor footprinting
  • A computer that runs on Unix-like system

Workshop participation

A mini-lecture will be given at the beginning that will cover the basics about ATAC-seq technology as well as a brief comparison to alternatives. Then, the major steps involved in ATAC-seq assay will be discussed along with the commonly practiced software tools, specifically, the usage of the package ATACseqQC for post-alignment QC will be demonstrated. Last will be a Q/A section.

R / Bioconductor main packages used

  • ATACseqQC [1]
  • ChIPpeakAnno [2]

Time outline

Activity Time
Overview of the workshop 2m
* Acknowledgments
* Agenda
* Setup of demo environment
Intro to ATAC-seq technology 5m
A typical ATAC-seq workflow 3m
Best practices 10m
* Important steps
* QCs
* Commonly used tools
Downstream analysis with ATACseqQC 15m
* Demo datasets
* Post-alignment QCs
* Demonstration
Q/A section 10m

Workshop goals and objectives

Learning goals

  • Be able to describe the basic ideas behind ATAC-seq
  • Get familiar with the commonly practiced tools used in ATAC-seq analysis

Learning objectives

  • Get familiar with the package ATACseqQC
  • Perform diagnostic plotting of ATAC-seq data

Workshop slides, video clip, and demo codes

Slides

  • inst/vignettes/IntegratedATACseqAnalysisWorkshop2021.pdf

Video clip

  • to be added

Demo codes

  • inst/vignettes/demo.R
  • inst/vignettes/demo.Rmd
  • inst/vignettes/demo.html

References

[1] https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html

[2] https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html