Path: blob/main/learning-pathways/epigenetics-from-zero.md
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---layout: learning-pathway tags: [beginner, genomic-intervals, epigenetics] cover-image: assets/images/chipseq-viz.png cover-image-alt: "Plot of ChIP-Seq signal from multiple samples across a genome region" type: use editorial_board: - wm75 - pavanvidem title: Epigenetics data analysis with Galaxy description: | Familiarize yourself with the Galaxy user interface and its most important features, then move on to analysis of genomic interval and deep-sequencing data with tools and tool suites like MACS2, bedtools and deepTools. priority: 9 pathway: - section: "Module 1: Introduction to Galaxy" description: | Get a first look at the Galaxy platform for data analysis. We start with a short introduction (video slides & practical) to familiarize you with the Galaxy interface, then proceed with slightly longer, but still introductory tutorials that demonstrate the handling of genomic intervals data in Galaxy. tutorials: - name: galaxy-intro-short topic: introduction - name: galaxy-intro-101 topic: introduction - name: galaxy-intro-peaks2genes topic: introduction - section: "Module 2: Analysis of ChIP-Seq, CUT&RUN and ATAC-Seq data" description: | Learn how to perform mapping, peak calling with **MACS-2**, read depth analysis and correlation with the **deepTools** suite, and results vizualization with **IGV** and other tools for various chromatin selection assays. tutorials: - name: formation_of_super-structures_on_xi topic: epigenetics - name: cut_and_run topic: epigenetics - name: atac-seq topic: epigenetics - section: "Module 3: Analysis of DNA modification" description: | Learn how to detect DNA methylation through sequencing and to analyze its distribution across genome regions. tutorials: - name: introduction-dna-methylation topic: epigenetics - name: methylation-seq topic: epigenetics
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