1906

LICENSE

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+MIT License
+
+Copyright (c) 2019 NBIS -- National Bioinformatics Infrastructure Sweden
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# course_rnaseq_slu
+
+This repo contains the course material for NBIS course **Workshop on RNA-Seq** at SLU. The rendered view of this repo is available [here](https://nbisweden.github.io/course_rnaseq_slu/).
+
+## Contributing
+
+To add or update contents of this repo (for collaborators), first clone the repo.
+
+```
+git clone https://github.com/nbisweden/course_rnaseq_slu.git
+```
+
+Make changes/updates as needed. Add the changed files. Commit it. Then push the repo back.
+
+```
+git add *
+git commit -m "I did this and that"
+git status
+git push origin
+```
+
+If you are not added as a collaborator, first fork this repo to your account, then clone it locally, make changes, commit, push to your repo, then submit a pull request to this repo.
+
+## Descriptions
+
+These are descriptions of the files and a guide to updating this repo for course maintainers.
+
+**_site.yml**  
+All website configuration options are here. Nothing to be changed here.
+
+**README.md**  
+You are reading this file now. Nothing to do here.
+
+**index.Rmd**  
+This file generates the home page. **Make sure that the date and location is correct**. Verify links.
+
+**schedule.Rmd**  
+This file generates the schedule page. **The start time of the course is set to `09:00:00`. Change if needed**. It is assumed that the course starts at the same time everyday.  
+
+**schedule.csv**  
+This table holds the schedule information. Open/edit in a spreadsheet or text editor. Columns are delimited by `;`. Do not change the number of columns, position of columns or column names.
+
+***date***: Full date for each day in format dd/mm/yyyy. Missing/empty cells are filled down automatically.  
+***room***: Room number for the course. Missing/empty cells are filled down automatically.  
+***dur***: Duration for the topic in minutes.  
+***topic***: Topic name (Keep it short).  
+***person***: Name of the person covering the topic.  
+***link_presentation***: (Optional) Link to the presentation. Local links can be just `presentation_topic.html`. Use this labelling convention.  
+***link_lab***: (Optional) Link to the lab material. Local links can be just `lab_topic.html`. This is the labelling convention used.  
+***link_room***: (Optional) Link to the room location. Can be a google map link, mazemap link etc.  
+
+**lab.Rmd**  
+This page brings together all the exercises. Verify links.
+
+**precourse.Rmd**  
+This page holds the steps needed to be completed before the course. **Change project ID for each course**.
+
+**info.Rmd**  
+This page contains practical information related to the course. **Set location and update info if needed**.
+
+[**presentation_topic.Rmd**]  
+RMarkdown presentation files for various topics. Replace 'topic' with a short name of the topic.  
+
+[**lab_topic.Rmd**]  
+RMarkdown lab files for various topics. Replace 'topic' with a short name of the topic. Check if paths to data is correct.  
+
+## Dependencies
+
+The `assets` directory contains css styles, headers, footers, logos etc. If you are using images in your .Rmd file, place them in the directory `images` and refer to them using relative path like `![](./images/image.jpg)`. Images generated in R during rendering of the .Rmd file is automatically handled. If you have data (tsv, csv, txt text files, .Rds files), place them inside the directory `data` and read them using relative path `x <- read.delim("./data/table.txt")`. Do not use paths that link outside of the project environment.
+
+## Rendering
+
+The website is rendered by running `rmarkdown::render_site()` in the project directory. This generates the HTML files and all other necessary files (including the assets, images and data directories) and moves them into a directory named **docs**. Open **docs/index.html** to start. The output directory is set to **docs** because this GitHub repo uses the **docs** directory as the Github pages (rendered content) source.
+
+For testing purposes, you can run `rmarkdown::render("bla.Rmd")` on individual Rmd files. This is a time-saver as the whole website need not be rendered just to preview this one file.
+
+---
+
+**2019** NBIS | SciLifeLab

_site.yml

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+name: Workshop on RNA-Seq
+favicon: assets/favicon.png
+output_dir: docs
+exclude: ["data","docs","README.md","schedule.csv"]
+navbar:
+  title: "<b>NBIS • Workshop on RNA-Seq</b>"
+  logo:
+    image: "assets/logo-white.svg"
+    href: https://nbisweden.github.io/course_rnaseq_slu
+  right:
+    - text: Home
+      icon: fa-home
+      href: index.html
+    - text: Schedule
+      icon: fa-clipboard-list
+      href: schedule.html
+    - text: Lab
+      icon: fa-flask
+      href: lab.html
+    - text: Precourse
+      icon: fa-pencil-alt
+      href: precourse.html
+    - text: Info
+      icon: fa-info
+      href: info.html
+output:
+  bookdown::html_document2:
+    theme: flatly
+    highlight: tango
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html

advanced-linux-answers.Rmd

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+---
+title: "Advanced Linux Answers"
+subtitle: "Workshop on RNA-Seq"
+author: "Martin Dahlö"
+output:
+  bookdown::html_document2:
+          toc: true
+          toc_float: true
+          toc_depth: 4
+          number_sections: true
+          theme: flatly
+          highlight: tango
+          df_print: default
+          code_folding: "none"
+          self_contained: false
+          keep_md: false
+          encoding: 'UTF-8'
+          css: "assets/lab.css"
+---
+
+```{r,child="assets/header-lab.Rmd"}
+```
+
+# Ownership and permissions
+
+Q:  Change permission from `----------` to `-rw-rw—wx`.
+
+One answer:
+
+```
+chmod ug+rw filename  
+chmod o+wx filename  
+```
+
+# Symbolic links - files
+
+Q Did editing the information in the link change the information in the original?  
+A: Yes.
+
+Q: What happens to a symbolic link when we move whatever its pointing to?  
+A: it breaks.
+
+Q: Is the link re-activated?  
+A: yes.
+
+# Grep
+
+Command to grep all lines with chr1 and send to other file.
+
+ex:
+
+```
+grep "chr1" sample_1.sam > chr1.txt
+```
+
+# WC
+
+```
+grep "chr1" sample_1.sam | wc -l
+samtools view outbam.bam | grep "CATCATCAT" | wc -l
+```
+
+# Extra material 1
+
+Task 1:
+
+```
+grep "^@" sample_1.sam > at.txt
+```
+
+Task 2:
+
+```
+grep "[0-9]\{3\}$" sample_1.sam
+```
+
+# Extra material 2
+
+```
+sed 's/chr1/chr2/' sample_1.sam > sample_2.sam
+```
+
+# Extra material 3
+
+```
+for f in *.sam; do mv $f ${f/.sam}.bam; done
+```
+
+__End of document__

advanced-linux-answers.md

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+---
+layout: default
+title:  'Advanced Linux Answers'
+---
+
+# Advlinux, cheat sheet
+
+#### Assignment – Ownership and permissions
+
+Q:  
+Change permission from 
+
+```bash
+----------
+```
+
+to
+
+```bash
+-rw-rw—wx
+```
+
+One answer:
+
+```bash
+chmod ug+rw filename  
+chmod o+wx filename  
+```
+
+#### Assignment - Symbolic links - files
+Q Did editing the information in the link change the information in the original?  
+A: Yes.
+
+Q: what happens to a symbolic link when we move whatever its pointing to?  
+A: it breaks.
+
+Q: is the link re-activated?  
+A: yes.
+
+#### Assignments - Grep
+command to grep all lines with chr1 and send to other file.
+
+ex:
+
+```bash
+grep "chr1" sample_1.sam > chr1.txt
+```
+
+#### Assignment - WC
+
+```bash
+grep "chr1" sample_1.sam | wc -l
+samtools view outbam.bam | grep "CATCATCAT" | wc -l
+```
+
+#### Extra material 1.
+Task1:
+
+```bash
+grep "^@" sample_1.sam > at.txt
+```
+
+Task2:
+
+```bash
+grep "[0-9]\{3\}$" sample_1.sam
+```
+
+#### Extra material 2.
+
+```bash
+sed 's/chr1/chr2/' sample_1.sam > sample_2.sam
+```
+
+#### Extra material 3
+
+```bash
+for f in *.sam; do mv $f ${f/.sam}.bam; done
+```