Introduction to ChIP-Seq Using Galaxy: Analysing protein interactions with DNA

Overview

Chromatin Immunoprecipiation (ChIP) allows us to identify DNA sequences bound by particular proteins. This provides a powerful way to investigate chromatin-associated proteins such as transcription factors. Recent advances in high throughput sequencing allow ChIP data to be analysed more accurately than before. However, carrying out this analysis requires knowledge of the bioinformatic tools involved with ChIP-Seq. This course will demonstrate these techniques, following the analysis used in published research articles.

Full course syllabus

  • Logging into the Galaxy Server.
  • Alignment of ChIP-Seq reads using Bowtie.
  • Visualising alignments in the Integrated Genome Viewer.
  • Using MACS to identify peaks of enrichment.
  • Analysing results.
  • Using MEME to extract consensus motifs.

Scientific topics: ChIP-seq

Keywords: Roslin Institute

Target audience: Any student, postdoc or RA who has an interest in bioinformatics and who intends to conduct ChIP-Seq analysis on a Galaxy platform.

Difficulty level: Intermediate

Licence: Other (Not Open)

Authors: Anmol J. Hemrom

Introduction to ChIP-Seq Using Galaxy: Analysing protein interactions with DNA https://tess.elixir-europe.org/materials/introduction-to-chip-seq-using-galaxy-analysing-protein-interactions-with-dna ChIP-sequencing, also known as ChIP-Seq, is a powerful technique for investigating protein interactions with DNA. This course will take you through an example ChIP-Seq analysis pipeline, following a published methodology to show how we can understand and reproduce these published results. ChIP-seq Roslin Institute Any student, postdoc or RA who has an interest in bioinformatics and who intends to conduct ChIP-Seq analysis on a Galaxy platform.