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2024.3/course_material/group_work/group_work/index.html

@@ -582,7 +582,7 @@ <h2 id="roles-organisation">Roles &amp; organisation</h2>
 <p>Each project has <strong>tasks</strong> and <strong>questions</strong>. By performing the tasks, you should be able to answer the questions. At the start of the project, make sure that each of you gets a task assigned. You should consider the tasks and questions as a guidance. If interesting questions pop up during the project, you are <strong>encouraged</strong> to work on those. Also, you don&rsquo;t have to perform all the tasks and answer all the questions.</p>
 <p>In the afternoon of day 1, you will divide the initial tasks, and start on the project. On day 2, you can work on the project in the morning and in the first part of the afternoon. We will conclude the projects with a <strong>10-minute presentation</strong> of each group.</p>
 <h2 id="working-directories">Working directories</h2>
-<p>Each group has access to a shared working directory. It is mounted in the root directory (<code>/</code>). </p>
+<p>Each group has access to a shared working directory. It is mounted in the root directory (<code>/group_work/groupX</code>). You can add the group work directory to the workspace in VScode by opening the menu on the top right (hamburger symbol), click <strong>File</strong> &gt; <strong>Add folder to workspace</strong> and type the path to the group work directory.</p>
 
 
 

2024.3/course_material/group_work/project1/index.html

@@ -561,8 +561,10 @@ <h1>Project 1</h1>
 
 <h2 id="project-1-differential-isoform-expression-analysis-of-ont-data"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M184 0c30.9 0 56 25.1 56 56v400c0 30.9-25.1 56-56 56-28.9 0-52.7-21.9-55.7-50.1-5.2 1.4-10.7 2.1-16.3 2.1-35.3 0-64-28.7-64-64 0-7.4 1.3-14.6 3.6-21.2C21.4 367.4 0 338.2 0 304c0-31.9 18.7-59.5 45.8-72.3C37.1 220.8 32 207 32 192c0-30.7 21.6-56.3 50.4-62.6C80.8 123.9 80 118 80 112c0-29.9 20.6-55.1 48.3-62.1 3-28 26.8-49.9 55.7-49.9zm144 0c28.9 0 52.6 21.9 55.7 49.9C411.5 56.9 432 82 432 112c0 6-.8 11.9-2.4 17.4 28.8 6.2 50.4 31.9 50.4 62.6 0 15-5.1 28.8-13.8 39.7 27.1 12.8 45.8 40.4 45.8 72.3 0 34.2-21.4 63.4-51.6 74.8 2.3 6.6 3.6 13.8 3.6 21.2 0 35.3-28.7 64-64 64-5.6 0-11.1-.7-16.3-2.1-3 28.2-26.8 50.1-55.7 50.1-30.9 0-56-25.1-56-56V56c0-30.9 25.1-56 56-56z"/></svg></span> Project 1: Differential isoform expression analysis of ONT data</h2>
 <p>In this project, you will be working with data from the same resource as the data we have already worked on:</p>
-<p>Clark, M. B. et al (2020). <em>Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain</em>. Molecular Psychiatry, 25(1), 37–47. <a href="https://doi.org/10.1038/s41380-019-0583-1">https://doi.org/10.1038/s41380-019-0583-1</a>.</p>
-<p>It is Oxford Nanopore Technology sequencing data of PCR amplicons of the gene CACNA1C. It is primarily used to discover new splice variants. We will use the dataset to do that and in addition do a differential isoform expression analysis with <a href="https://github.com/BrooksLabUCSC/flair">FLAIR</a>.</p>
+<blockquote>
+<p>Padilla, Juan-Carlos A., Seda Barutcu, Ludovic Malet, Gabrielle Deschamps-Francoeur, Virginie Calderon, Eunjeong Kwon, and Eric Lécuyer. “Profiling the Polyadenylated Transcriptome of Extracellular Vesicles with Long-Read Nanopore Sequencing.” BMC Genomics 24, no. 1 (September 22, 2023): 564. https://doi.org/10.1186/s12864-023-09552-6.</p>
+</blockquote>
+<p>It is Oxford Nanopore Technology sequencing data of cDNA from extracellular vesicles and whole cells. It is primarily used to discover new splice variants. We will use the dataset to do that and in addition do a differential isoform expression analysis with <a href="https://github.com/BrooksLabUCSC/flair">FLAIR</a>.</p>
 <div class="admonition info">
 <p class="admonition-title">Project aim</p>
 <p>Discover new splice variants and identify differentially expressed isoforms.</p>
@@ -574,43 +576,25 @@ <h2 id="project-1-differential-isoform-expression-analysis-of-ont-data"><span cl
 </code></pre></div>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>Download the data file package in your shared working directory, i.e. : <code>/group_work/&lt;group name&gt;</code> or <code>~/&lt;group name&gt;</code>. Only one group member has to do this.</p>
+<p>Download the data file package in your shared working directory, i.e. : <code>/group_work/&lt;group name&gt;</code>. Only one group member has to do this. You can add the group work directory to the workspace in VScode by opening the menu on the top right (hamburger symbol), click <strong>File</strong> &gt; <strong>Add folder to workspace</strong> and type the path to the group work directory.</p>
 </div>
 <p>This will create a directory <code>project1</code> with the following structure:</p>
 <div class="highlight"><pre><span></span><code>project1/
-├── alignments
-│   ├── cerebellum-5238-batch2.bam
-│   ├── cerebellum-5298-batch2.bam
-│   ├── cerebellum-5346-batch2.bam
-│   ├── parietal_cortex-5238-batch1.bam
-│   ├── parietal_cortex-5298-batch1.bam
-│   └── parietal_cortex-5346-batch1.bam
-├── counts
-│   └── counts_matrix_test.tsv
 ├── reads
-│   ├── cerebellum-5238-batch2.fastq.gz
-│   ├── cerebellum-5298-batch2.fastq.gz
-│   ├── cerebellum-5346-batch2.fastq.gz
-│   ├── parietal_cortex-5238-batch1.fastq.gz
-│   ├── parietal_cortex-5298-batch1.fastq.gz
-│   ├── parietal_cortex-5346-batch1.fastq.gz
-│   ├── striatum-5238-batch2.fastq.gz
-│   ├── striatum-5298-batch2.fastq.gz
-│   └── striatum-5346-batch2.fastq.gz
+│   ├── Cell_1.fastq.gz
+│   ├── Cell_2.fastq.gz
+│   ├── Cell_3.fastq.gz
+│   ├── EV_1.fastq.gz
+│   ├── EV_2.fastq.gz
+│   └── EV_3.fastq.gz
 ├── reads_manifest.tsv
-└── scripts
-    └── differential_expression_example.Rmd
+└── references
+    ├── Homo_sapiens.GRCh38.111.chr5.chr6.chrX.gtf
+    └── Homo_sapiens.GRCh38.dna.primary_assembly.chr5.chr6.chrX.fa
 
-4 directories, 18 files
-</code></pre></div>
-<p>Download the fasta file and gtf like this:</p>
-<div class="highlight"><pre><span></span><code><span class="nb">cd</span><span class="w"> </span>project1/
-mkdir<span class="w"> </span>reference
-<span class="nb">cd</span><span class="w"> </span>reference
-wget<span class="w"> </span>ftp://ftp.ensembl.org/pub/release-102/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.12.fa.gz
-wget<span class="w"> </span>ftp://ftp.ensembl.org/pub/release-102/gtf/homo_sapiens/Homo_sapiens.GRCh38.102.gtf.gz
-gunzip<span class="w"> </span>*.gz
+2 directories, 9 files
 </code></pre></div>
+<p>In the reads folder a fastq file with reads, which are described in <code>reads_manifest.csv</code>. EV means &lsquo;extracellular vesicle&rsquo;, Cell means &lsquo;entire cells&rsquo;. In the references folder you can find the reference sequence and annotation.</p>
 <h3 id="before-you-start">Before you start</h3>
 <p>You can start this project with dividing initial tasks. Because some intermediate files are already given, participants can develop scripts/analyses at different steps of the full analysis from the start. Possible starting points are:</p>
 <ul>