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home_contents.qmd
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---
title: "Contents"
description: "Course materials organised by topic. When following a live workshop, use **Schedule**.<br>Slides: {{< fa file-powerpoint >}} / {{< fa file-pdf >}}, Labs: {{< fa file-lines >}}, Videos: {{< fa brands youtube >}}"
date: ""
toc: false
number-sections: false
sidebar: false
format: html
---
### Introduction to Linux
- Introduction to Linux [{{< fa brands youtube >}}](https://youtu.be/qYp8shSMJ-0) [{{< fa file-pdf >}}](topics/linux/slide_linux_intro.pdf) [{{< fa file-lines >}}](topics/linux/lab_linux_intro.html)
- Linux file permissions [{{< fa file-lines >}}](topics/linux/lab_linux_permissions.html)
### High-Performance Computing cluster
- Introduction to HPC [{{< fa brands youtube >}}](https://youtu.be/cxEtfKN91q4) [{{< fa file-pdf >}}](topics/hpc/intro/slide_hpc_intro.pdf) [{{< fa file-lines >}}](topics/hpc/intro/lab_intro.html)
- HPC Pipelines [{{< fa file-lines >}}](topics/hpc/pipeline/lab_pipeline.html)
### File types in Linux
- File types in Bioinformatics [{{< fa brands youtube >}}](https://youtu.be/7MR1qUZQ94w) [{{< fa file-pdf >}}](topics/linux/slide_linux_filetypes.pdf) [{{< fa file-lines >}}](topics/linux/lab_linux_filetypes.html)
### Advanced Linux
- Better terminal experience [{{< fa brands youtube >}}](https://youtu.be/RGbONVWOaDo) [{{< fa file-pdf >}}](topics/linux/slide_qol_termexp.pdf)
- Advanced Linux [{{< fa brands youtube >}}](https://youtu.be/n3IpUHIodM8) [{{< fa file-pdf >}}](topics/linux/slide_linux_advanced.pdf) [{{< fa file-lines >}}](topics/linux/lab_linux_advanced.html)
### Variant-calling workflow
- Variant-calling [{{< fa brands youtube >}}](https://youtu.be/NxRECdxKP40) [{{< fa file-powerpoint >}}](topics/vc/slide_vc.pptx) [{{< fa file-lines >}}](topics/vc/lab_vc.html)
<!-- [Variant-calling Lab answers](lab_vc_answers.pdf)-->
### RNA-Seq workflow
- RNA-Seq workflow [{{< fa brands youtube >}}](https://youtu.be/gC_nslHgSa8) [{{< fa brands html5 >}}](topics/rnaseq/slide_rnaseq.html) [{{< fa file-lines >}}](topics/rnaseq/lab_rnaseq.html)
- Simon's report [{{< fa file-lines >}}](topics/rnaseq/simon-report/validating_knockout.html)
### NGS technologies
- NGS technologies and challenges [{{< fa brands youtube >}}](https://youtu.be/5sUzkrucL1E) [{{< fa file-pdf >}}](topics/other/slide_sequencing.pdf)
- NGS Pipelines [{{< fa brands youtube >}}](https://youtu.be/6RBhfMvDkSI) [{{< fa file-pdf >}}](topics/other/slide_ngs_pipelines.pdf)
### Other
- QC of FastQ reads [{{< fa file-pdf >}}](topics/other/slide_qc.pdf) [{{< fa file-lines >}}](topics/other/lab_qc.html)
- Data management [{{< fa brands youtube >}}](https://youtu.be/PfcrDlhY1zE) [{{< fa file-powerpoint >}}](topics/other/slide_data_management.pdf)
### Useful resources
- Connecting to HPC PDC [{{< fa file-lines >}}](topics/other/lab_connect_pdc.html)
- Connecting to HPC UPPMAX [{{< fa file-lines >}}](topics/other/lab_connect_uppmax.html)
- Uploading & downloading files from HPC [{{< fa file-lines >}}](topics/other/lab_download_files.html)
- Working on Tetralith: The backup cluster [{{< fa file-lines >}}](topics/other/lab_tetralith.html)
- Linux cheatsheet [{{< fa file-pdf >}}](topics/linux/assets/linux_cheat_sheet.pdf)
- Bash cheat sheet 1 [{{< fa file-pdf >}}](topics/linux/assets/bash_cheat_sheet_1.pdf)
- Bash cheat sheet 2 [{{< fa file-pdf >}}](topics/linux/assets/bash_cheat_sheet_2.pdf)
- Bash cheat sheet 3 [{{< fa file-pdf >}}](topics/linux/assets/bash_cheat_sheet_3.pdf)
- Uppmax cheatsheet [{{< fa file-image >}}](topics/linux/assets/uppmax_cheat_sheet.png)
- Mac keyboard [{{< fa file-lines >}}](topics/other/lab_mac_keyboard.html)