Introduction to Bioinformatics using NGS data
Description
An introductory workshop on applied bioinformatic next-generation sequence analyses run by the National Bioinformatic Infrastructure Sweden (NBIS) in partnership with National Genomics Infrastructure (NGI).
This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 3000 SEK. Please note that NBIS cannot invoice individuals.
Briefly, the workshop covers the followings major topics:
- Working on the UNIX/LINUX command line
- Bioinformatic/NGS data formats and QC
- DNA variant calling workflow essentials
- RNA sequence analysis workflow essentials
A more detailed syllabus is here:
- 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 HPC
- 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
Content Providers
Learning Outcomes
- 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.
Prerequisites & Technical Requirements
Prerequisites
This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare.
Required to be able to follow the tutorials:
- BYOL, bring your own laptop configured according to precourse instructions.
- A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable.
To get the maximum benefit from the workshop:
- Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.
If we receive more applications than we have seats in the course, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers. International applicants are accepted based on availability of seats.
Technical requirements
Applicants are expected to bring their own laptops. A reasonably modern laptop with linux/unix, mac or windows OS and internet connection. No system requirements are set since we only use the laptop to connect to a remote cluster where we work.
Topics & Tags
Affiliations & Networks
Activity log
