Lecture slides
1
General processing of NGS data
Epigenomics Workshop
Source Code
Browse version `devel`
Welcome
Program
Prerequisites
Lecture slides
1
General processing of NGS data
2
Quantification of gene expression
3
Introduction to general epigenomics concepts
4
ATAC-seq peak calling and visualization
5
Introduction to ChIP-seq processing and analysis
6
DNA motif methodologies and resources
7
Profiling chromatin contacts and visualize Hi-C data
8
Identifying structural features from Hi-C data
9
Integrating multi-omics data through GO analysis
Hands-on exercises
10
Lab 1: Hands-on processing of RNA-seq
11
Lab 2: Quantification and differential gene expression by RNA-seq
12
Lab 3: Processing MNase-seq data
13
Lab 4: ATAC-seq analysis
14
Lab 5: Comparing sets of ChIP-seq peaks
15
Lab 6: Motif enrichment analysis from ChIP-seq data
16
Lab 7: Hi-C data processing
17
Lab 8: Investigating Hi-C contact maps
18
Lab 9: Multi-omics data integration
Appendices
Extra resources
Lecture slides
1
General processing of NGS data
1
General processing of NGS data
<div id="quarto-navigation-envelope" class="hidden"> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar-title">Epigenomics Workshop</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-navbar-title">Epigenomics Workshop</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-next"><span class="chapter-number">2</span> <span class="chapter-title">Quantification of gene expression</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-prev">Prerequisites</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/index.htmlWelcome">Welcome</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/program.htmlProgram">Program</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/prerequisites.htmlPrerequisites">Prerequisites</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:quarto-sidebar-section-1">Lecture slides</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lecture1.html<span-class='chapter-number'>1</span>--<span-class='chapter-title'>General-processing-of-NGS-data</span>"><span class="chapter-number">1</span> <span class="chapter-title">General processing of NGS data</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lecture2.html<span-class='chapter-number'>2</span>--<span-class='chapter-title'>Quantification-of-gene-expression</span>"><span class="chapter-number">2</span> <span class="chapter-title">Quantification of gene expression</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lecture3.html<span-class='chapter-number'>3</span>--<span-class='chapter-title'>Introduction-to-general-epigenomics-concepts</span>"><span class="chapter-number">3</span> <span class="chapter-title">Introduction to general epigenomics concepts</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lecture4.html<span-class='chapter-number'>4</span>--<span-class='chapter-title'>ATAC-seq-peak-calling-and-visualization</span>"><span class="chapter-number">4</span> <span class="chapter-title">ATAC-seq peak calling and visualization</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lecture5.html<span-class='chapter-number'>5</span>--<span-class='chapter-title'>Introduction-to-ChIP-seq-processing-and-analysis</span>"><span class="chapter-number">5</span> <span class="chapter-title">Introduction to ChIP-seq processing and analysis</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lecture6.html<span-class='chapter-number'>6</span>--<span-class='chapter-title'>DNA-motif-methodologies-and-resources</span>"><span class="chapter-number">6</span> <span class="chapter-title">DNA motif methodologies and resources</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lecture7.html<span-class='chapter-number'>7</span>--<span-class='chapter-title'>Profiling-chromatin-contacts-and-visualize-Hi-C-data</span>"><span class="chapter-number">7</span> <span class="chapter-title">Profiling chromatin contacts and visualize Hi-C data</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lecture8.html<span-class='chapter-number'>8</span>--<span-class='chapter-title'>Identifying-structural-features-from-Hi-C-data</span>"><span class="chapter-number">8</span> <span class="chapter-title">Identifying structural features from Hi-C data</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lecture9.html<span-class='chapter-number'>9</span>--<span-class='chapter-title'>Integrating-multi-omics-data-through-GO-analysis</span>"><span class="chapter-number">9</span> <span class="chapter-title">Integrating multi-omics data through GO analysis</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:quarto-sidebar-section-2">Hands-on exercises</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lab1.html<span-class='chapter-number'>10</span>--<span-class='chapter-title'>Lab-1:-Hands-on-processing-of-RNA-seq</span>"><span class="chapter-number">10</span> <span class="chapter-title">Lab 1: Hands-on processing of RNA-seq</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lab2.html<span-class='chapter-number'>11</span>--<span-class='chapter-title'>Lab-2:-Quantification-and-differential-gene-expression-by-RNA-seq</span>"><span class="chapter-number">11</span> <span class="chapter-title">Lab 2: Quantification and differential gene expression by RNA-seq</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lab3.html<span-class='chapter-number'>12</span>--<span-class='chapter-title'>Lab-3:-Processing-MNase-seq-data</span>"><span class="chapter-number">12</span> <span class="chapter-title">Lab 3: Processing MNase-seq data</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lab4.html<span-class='chapter-number'>13</span>--<span-class='chapter-title'>Lab-4:-ATAC-seq-analysis</span>"><span class="chapter-number">13</span> <span class="chapter-title">Lab 4: ATAC-seq analysis</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lab5.html<span-class='chapter-number'>14</span>--<span-class='chapter-title'>Lab-5:-Comparing-sets-of-ChIP-seq-peaks</span>"><span class="chapter-number">14</span> <span class="chapter-title">Lab 5: Comparing sets of ChIP-seq peaks</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lab6.html<span-class='chapter-number'>15</span>--<span-class='chapter-title'>Lab-6:-Motif-enrichment-analysis-from-ChIP-seq-data</span>"><span class="chapter-number">15</span> <span class="chapter-title">Lab 6: Motif enrichment analysis from ChIP-seq data</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lab7.html<span-class='chapter-number'>16</span>--<span-class='chapter-title'>Lab-7:-Hi-C-data-processing</span>"><span class="chapter-number">16</span> <span class="chapter-title">Lab 7: Hi-C data processing</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lab8.html<span-class='chapter-number'>17</span>--<span-class='chapter-title'>Lab-8:-Investigating-Hi-C-contact-maps</span>"><span class="chapter-number">17</span> <span class="chapter-title">Lab 8: Investigating Hi-C contact maps</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/Lab9.html<span-class='chapter-number'>18</span>--<span-class='chapter-title'>Lab-9:-Multi-omics-data-integration</span>"><span class="chapter-number">18</span> <span class="chapter-title">Lab 9: Multi-omics data integration</span></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:quarto-sidebar-section-3">Appendices</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-int-sidebar:/pages/extra.htmlExtra-resources">Extra resources</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-breadcrumbs-Lecture-slides">Lecture slides</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-breadcrumbs-<span-class='chapter-number'>1</span>--<span-class='chapter-title'>General-processing-of-NGS-data</span>"><span class="chapter-number">1</span> <span class="chapter-title">General processing of NGS data</span></span></p> <div class="hidden quarto-markdown-envelope-contents" data-render-id="footer-left"> <p>This book was built with <a href="https://github.com/js2264/BiocBook/">BiocBook</a> with <span class="emoji" data-emoji="heart">❤️</span></p> </div> </div> <div id="quarto-meta-markdown" class="hidden"> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-metatitle"><span class="chapter-number">1</span> <span class="chapter-title">General processing of NGS data</span> – Epigenomics Workshop</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-twittercardtitle"><span class="chapter-number">1</span> <span class="chapter-title">General processing of NGS data</span> – Epigenomics Workshop</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-ogcardtitle"><span class="chapter-number">1</span> <span class="chapter-title">General processing of NGS data</span> – Epigenomics Workshop</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-metasitename">Epigenomics Workshop</span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-twittercarddesc"></span> <span class="hidden quarto-markdown-envelope-contents" data-render-id="quarto-ogcardddesc"></span></p> </div>
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Prerequisites
2
Quantification of gene expression