home_syllabus.qmd

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title: "Syllabus"
subtitle: "This workshop is aimed towards biologists, researchers, computer scientists or data analysts with limited experience in analysing NGS data."
date: ""
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## Syllabus

The syllabus for this workshop are as follows.

- Working on the unix/linux command line
  - Command line navigation and related commands: cd, mkdir, rm, rmdir
  - Commonly used linux tools: cp, mv, tar, less, more, head, tail, nano, grep, top, man
  - Wildcards
  - Ownership and permissions
  - Symbolic links
  - Piping commands
- Working on remote computing cluster
  - Logging on to UPPMAX
  - Booking resources
  - Job templates, submission and queues
  - Modules
- Commonly used bioinformatic tools and pipelines
- Working with integrated genome viewer
- Variant-calling workflow
  - Mapping reads to the reference genome
  - Variant detection
  - VCF file format
- RNA-Seq workflow
  - RNA-Seq experimental design and considerations
  - QC, mapping and gene expression counts
  - Differential gene expression analyses
- Current advances in NGS technologies

## Learning outcomes

After this workshop you should be able to:

- Describe the basic principles of next generation sequencing.
- Use the Linux command line interface to manage simple file processing operations, and organise directory structures.
- Connect to and work on a remote compute cluster.
- Apply programs in Linux for analysis of NGS data.
- Summarise the applications of current NGS technologies, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.
- Explain common NGS file formats.
- Interpret quality control of NGS reads.
- Explain the steps involved in variant calling using whole genome sequencing data.
- Independently perform a basic variant calling workflow on example data.
- Explain the steps involved in a differential gene expression workflow using RNA seq data.
- Hands-on experience with handling of raw RNA sequencing data, QC and quantification of gene expression.
- Conceptual understanding of differential gene expression analysis.

## Entry requirements

- This is a national course open to PhD students, postdocs, group leaders and core facility staff.

- A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to

- Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.
It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others.

- Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Applicants affiliated to a Swedish institution are prioritized. International applicants are considered only if/when seats are available. Further prioritization: PhD scholars > Post-Docs, PIs, Healthcare staff > Master's students).

- Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

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