Day 2
5
Lecture 3 - NGS processing workflows
Epigenomics Data Analysis
Welcome
Program
RStudio
Prerequisites
Day 1
1
Lecture 1 - Introduction to epigenomics data analysis
2
Lecture 2 - General processing of genome-wide epigenomic assays
3
Demo 1 - Processing of MNase-seq data
4
Lab 1 - Processing of MNase-seq data
Day 2
5
Lecture 3 - NGS processing workflows
6
Lecture 4 - ATAC-seq processing and analyis
7
Lecture 5 - R 101
8
Demo 2 - Processing of ATAC-seq data
9
Lab 2 - ATAC-seq downstream analysis
Day 3
10
Lecture 6 - ChIP-seq processing and analyis
11
Lecture 7 - R 201
12
Demo 3 - Processing of ChIP-seq data
13
Lab 3 - ChIP-seq downstream analysis
Day 4
14
Lecture 8 - RNA-seq processing and analyis
15
Lecture 9 - R 301
16
Demo 4 - Processing of RNA-seq data
17
Lab 4 - RNA-seq downstream analysis
Day 5
18
Lecture 10 - HiC processing
19
Lecture 11 - GO and GSEA analysis
20
Demo 5 - Leveraging Bioconductor resources
21
Lab 5 - Multi-omics data integration
Extra resources
5
Lecture 3 - NGS processing workflows
<div id="quarto-navigation-envelope" class="hidden"> <p><span class="hidden" data-render-id="quarto-int-sidebar-title">Epigenomics Data Analysis</span> <span class="hidden" data-render-id="quarto-int-navbar-title">Epigenomics Data Analysis</span> <span class="hidden" data-render-id="quarto-int-next"><span class="chapter-number">6</span> <span class="chapter-title">Lecture 4 - ATAC-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-int-prev"><span class="chapter-number">4</span> <span class="chapter-title">Lab 1 - Processing of MNase-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/index.html">Welcome</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/program.html">Program</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/Rstudio.html">RStudio</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/prerequisites.html">Prerequisites</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-1">Day 1</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture1_introduction.html"><span class="chapter-number">1</span> <span class="chapter-title">Lecture 1 - Introduction to epigenomics data analysis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture2_processing.html"><span class="chapter-number">2</span> <span class="chapter-title">Lecture 2 - General processing of genome-wide epigenomic assays</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Demo1_MNase-seq_processing.html"><span class="chapter-number">3</span> <span class="chapter-title">Demo 1 - Processing of MNase-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lab1_MNase-seq_processing.html"><span class="chapter-number">4</span> <span class="chapter-title">Lab 1 - Processing of MNase-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-2">Day 2</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture3_workflows.html"><span class="chapter-number">5</span> <span class="chapter-title">Lecture 3 - NGS processing workflows</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture4_ATACseq.html"><span class="chapter-number">6</span> <span class="chapter-title">Lecture 4 - ATAC-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture5_R-101.html"><span class="chapter-number">7</span> <span class="chapter-title">Lecture 5 - R 101</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Demo2_ATAC-seq_processing.html"><span class="chapter-number">8</span> <span class="chapter-title">Demo 2 - Processing of ATAC-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lab2_ATAC-seq_analysis.html"><span class="chapter-number">9</span> <span class="chapter-title">Lab 2 - ATAC-seq downstream analysis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-3">Day 3</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lecture6_ChIPseq.html"><span class="chapter-number">10</span> <span class="chapter-title">Lecture 6 - ChIP-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lecture7_R-201.html"><span class="chapter-number">11</span> <span class="chapter-title">Lecture 7 - R 201</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Demo3_ChIP-seq_processing.html"><span class="chapter-number">12</span> <span class="chapter-title">Demo 3 - Processing of ChIP-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lab3_ChIP-seq_analysis.html"><span class="chapter-number">13</span> <span class="chapter-title">Lab 3 - ChIP-seq downstream analysis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-4">Day 4</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture8_RNAseq.html"><span class="chapter-number">14</span> <span class="chapter-title">Lecture 8 - RNA-seq processing and analyis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture9_R-301.html"><span class="chapter-number">15</span> <span class="chapter-title">Lecture 9 - R 301</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Demo4_RNA-seq_processing.html"><span class="chapter-number">16</span> <span class="chapter-title">Demo 4 - Processing of RNA-seq data</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lab4_RNA-seq_analysis.html"><span class="chapter-number">17</span> <span class="chapter-title">Lab 4 - RNA-seq downstream analysis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-5">Day 5</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lecture10_HiC.html"><span class="chapter-number">18</span> <span class="chapter-title">Lecture 10 - HiC processing</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lecture11_GO-GSEA.html"><span class="chapter-number">19</span> <span class="chapter-title">Lecture 11 - GO and GSEA analysis</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Demo5_Bioc-resources.html"><span class="chapter-number">20</span> <span class="chapter-title">Demo 5 - Leveraging Bioconductor resources</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lab5_data-integration.html"><span class="chapter-number">21</span> <span class="chapter-title">Lab 5 - Multi-omics data integration</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/extra.html">Extra resources</span> <span class="hidden" data-render-id="footer-left">Epigenomics Data Analysis |<br /> J. Serizay</span> <span class="hidden" data-render-id="footer-right">This book was built with <a href="https://quarto.org/">Quarto</a>.</span> <span class="hidden" data-render-id="quarto-breadcrumbs-5d0d9e50bf708684c2c6e57b56ae9e8c">Day 2</span> <span class="hidden" data-render-id="quarto-breadcrumbs-0f086f9cda352bd420bab354be080b39"><span class="chapter-number">5</span> <span class="chapter-title">Lecture 3 - NGS processing workflows</span></span></p> </div> <div id="quarto-meta-markdown" class="hidden"> <p><span class="hidden" data-render-id="quarto-metatitle">Epigenomics Data Analysis - <span class="chapter-number">5</span> <span class="chapter-title">Lecture 3 - NGS processing workflows</span></span> <span class="hidden" data-render-id="quarto-twittercardtitle">Epigenomics Data Analysis - <span class="chapter-number">5</span> <span class="chapter-title">Lecture 3 - NGS processing workflows</span></span> <span class="hidden" data-render-id="quarto-ogcardtitle">Epigenomics Data Analysis - <span class="chapter-number">5</span> <span class="chapter-title">Lecture 3 - NGS processing workflows</span></span> <span class="hidden" data-render-id="quarto-metasitename">Epigenomics Data Analysis</span> <span class="hidden" data-render-id="quarto-twittercarddesc"></span> <span class="hidden" data-render-id="quarto-ogcardddesc"></span></p> </div> </main> <!-- /main --> <script id = "quarto-html-after-body" type="application/javascript"> window.document.addEventListener("DOMContentLoaded", function (event) { const toggleBodyColorMode = (bsSheetEl) => { const mode = bsSheetEl.getAttribute("data-mode"); const bodyEl = window.document.querySelector("body"); if (mode === "dark") { bodyEl.classList.add("quarto-dark"); bodyEl.classList.remove("quarto-light"); } else { bodyEl.classList.add("quarto-light"); bodyEl.classList.remove("quarto-dark"); } } const toggleBodyColorPrimary = () => { const bsSheetEl = window.document.querySelector("link#quarto-bootstrap"); if (bsSheetEl) { toggleBodyColorMode(bsSheetEl); } } toggleBodyColorPrimary(); const icon = ""; const anchorJS = new window.AnchorJS(); anchorJS.options = { placement: 'right', icon: icon }; anchorJS.add('.anchored'); const isCodeAnnotation = (el) => { for (const clz of el.classList) { if (clz.startsWith('code-annotation-')) { return true; } } return false; } const clipboard = new window.ClipboardJS('.code-copy-button', { text: function(trigger) { const codeEl = trigger.previousElementSibling.cloneNode(true); for (const childEl of codeEl.children) { if (isCodeAnnotation(childEl)) { childEl.remove(); } } return codeEl.innerText; } }); clipboard.on('success', function(e) { // button target const button = e.trigger; // don't keep focus button.blur(); // flash "checked" button.classList.add('code-copy-button-checked'); var currentTitle = button.getAttribute("title"); button.setAttribute("title", "Copied!"); let tooltip; if (window.bootstrap) { button.setAttribute("data-bs-toggle", "tooltip"); button.setAttribute("data-bs-placement", "left"); button.setAttribute("data-bs-title", "Copied!"); tooltip = new bootstrap.Tooltip(button, { trigger: "manual", customClass: "code-copy-button-tooltip", offset: [0, -8]}); tooltip.show(); } setTimeout(function() { if (tooltip) { tooltip.hide(); button.removeAttribute("data-bs-title"); button.removeAttribute("data-bs-toggle"); button.removeAttribute("data-bs-placement"); } button.setAttribute("title", currentTitle); button.classList.remove('code-copy-button-checked'); }, 1000); // clear code selection e.clearSelection(); }); function tippyHover(el, contentFn) { const config = { allowHTML: true, content: contentFn, maxWidth: 500, delay: 100, arrow: false, appendTo: function(el) { return el.parentElement; }, interactive: true, interactiveBorder: 10, theme: 'quarto', placement: 'bottom-start' }; window.tippy(el, config); } const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]'); for (var i=0; i<noterefs.length; i++) { const ref = noterefs[i]; tippyHover(ref, function() { // use id or data attribute instead here let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href'); try { href = new URL(href).hash; } catch {} const id = href.replace(/^#\/?/, ""); const note = window.document.getElementById(id); return note.innerHTML; }); } let selectedAnnoteEl; const selectorForAnnotation = ( cell, annotation) => { let cellAttr = 'data-code-cell="' + cell + '"'; let lineAttr = 'data-code-annotation="' + annotation + '"'; const selector = 'span[' + cellAttr + '][' + lineAttr + ']'; return selector; } const selectCodeLines = (annoteEl) => { const doc = window.document; const targetCell = annoteEl.getAttribute("data-target-cell"); const targetAnnotation = annoteEl.getAttribute("data-target-annotation"); const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation)); const lines = annoteSpan.getAttribute("data-code-lines").split(","); const lineIds = lines.map((line) => { return targetCell + "-" + line; }) let top = null; let height = null; let parent = null; if (lineIds.length > 0) { //compute the position of the single el (top and bottom and make a div) const el = window.document.getElementById(lineIds[0]); top = el.offsetTop; height = el.offsetHeight; parent = el.parentElement.parentElement; if (lineIds.length > 1) { const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]); const bottom = lastEl.offsetTop + lastEl.offsetHeight; height = bottom - top; } if (top !== null && height !== null && parent !== null) { // cook up a div (if necessary) and position it let div = window.document.getElementById("code-annotation-line-highlight"); if (div === null) { div = window.document.createElement("div"); div.setAttribute("id", "code-annotation-line-highlight"); div.style.position = 'absolute'; parent.appendChild(div); } div.style.top = top - 2 + "px"; div.style.height = height + 4 + "px"; let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter"); if (gutterDiv === null) { gutterDiv = window.document.createElement("div"); gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter"); gutterDiv.style.position = 'absolute'; const codeCell = window.document.getElementById(targetCell); const gutter = codeCell.querySelector('.code-annotation-gutter'); gutter.appendChild(gutterDiv); } gutterDiv.style.top = top - 2 + "px"; gutterDiv.style.height = height + 4 + "px"; } selectedAnnoteEl = annoteEl; } }; const unselectCodeLines = () => { const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"]; elementsIds.forEach((elId) => { const div = window.document.getElementById(elId); if (div) { div.remove(); } }); selectedAnnoteEl = undefined; }; // Attach click handler to the DT const annoteDls = window.document.querySelectorAll('dt[data-target-cell]'); for (const annoteDlNode of annoteDls) { annoteDlNode.addEventListener('click', (event) => { const clickedEl = event.target; if (clickedEl !== selectedAnnoteEl) { unselectCodeLines(); const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active'); if (activeEl) { activeEl.classList.remove('code-annotation-active'); } selectCodeLines(clickedEl); clickedEl.classList.add('code-annotation-active'); } else { // Unselect the line unselectCodeLines(); clickedEl.classList.remove('code-annotation-active'); } }); } const findCites = (el) => { const parentEl = el.parentElement; if (parentEl) { const cites = parentEl.dataset.cites; if (cites) { return { el, cites: cites.split(' ') }; } else { return findCites(el.parentElement) } } else { return undefined; } }; var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]'); for (var i=0; i<bibliorefs.length; i++) { const ref = bibliorefs[i]; const citeInfo = findCites(ref); if (citeInfo) { tippyHover(citeInfo.el, function() { var popup = window.document.createElement('div'); citeInfo.cites.forEach(function(cite) { var citeDiv = window.document.createElement('div'); citeDiv.classList.add('hanging-indent'); citeDiv.classList.add('csl-entry'); var biblioDiv = window.document.getElementById('ref-' + cite); if (biblioDiv) { citeDiv.innerHTML = biblioDiv.innerHTML; } popup.appendChild(citeDiv); }); return popup.innerHTML; }); } } }); </script> <nav class="page-navigation"> <div class="nav-page nav-page-previous"> <a href="/content/day1/Lab1_MNase-seq_processing.html" class="pagination-link"> <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class='chapter-number'>4</span> <span class='chapter-title'>Lab 1 - Processing of MNase-seq data</span></span> </a> </div> <div class="nav-page nav-page-next"> <a href="/content/day2/Lecture4_ATACseq.html" class="pagination-link"> <span class="nav-page-text"><span class='chapter-number'>6</span> <span class='chapter-title'>Lecture 4 - ATAC-seq processing and analyis</span></span> <i class="bi bi-arrow-right-short"></i> </a> </div> </nav> </div> <!-- /content --> <footer class="footer"> <div class="nav-footer"> <div class="nav-footer-left"> <div class='footer-contents'>Epigenomics Data Analysis | J. Serizay </div> </div> <div class="nav-footer-center"> </div> <div class="nav-footer-right"> <div class='footer-contents'>This book was built with <a href="https://quarto.org/">Quarto</a>. </div> </div> </div> </footer> </body> </html>