Course in Advanced Bioinformatics

Table of Contents

• Course in Advanced Bioinformatics
  • Table of Contents
• Outline
• Shared point with students
• Software requirements
  • Running with our Docker Image
  • Running locally
• Some EXTRA recommendations
• Author
• Contributing

Outline

• Lecture 1: Introduction to genome sequencing and next generation sequencing methods.
• Lecture 2: Introduction to the Linux command line, NGS data formats, read mapping and alignments (hands-on available here).
• Lecture 3: NGS applications: RNA‐seq.
• Lecture 4: NGS applications: ChIP‐seq.
• Lecture 5: NGS applications: Variant detection, SNPs, CNVs, structural variants, epigenetic variation.
• Lecture 6: NGS applications: Sequence assembly, de‐novo sequencing and EST sequencing.
• Lecture 7: Introduction to Genome Browsing with the UCSC Genome Browser.

Shared point with students

Lessons and schedule available here.

Software requirements

Running with our Docker Image

• osvaldogc/ufv:2.0: Docker image with Hands On packages already installed. Images can be pulled via docker pull osvaldogc/ufv:2.0. Detailed instructions here.

Running locally

Remember that all the packages required to run the analysis are already installed in our Docker image.

Follow this guide if you want to run your analysis locally.

Some EXTRA recommendations

If you want to complement, add or step up your knowledge in bioinformatics...

• My June 27, 2022 post in FEBS Network: Why and how should you start learning bioinformatics?

Some deeper and longer... but highly recommended bioinformatics courses (still available online):

• Foundations of Computational and Systems Biology. MIT Opencourseware. Spring 2014.
• MIT CompBio. MIT. 2018.

Recommended books:

• Bioinformatics algorithms by Pavel A. Pevzner.
• Modern Statistics for Modern Biology by Susan Holmes and Wolfgang Huber.

Author

Fernando Pozo – @fpozoca - Google Scholar – fpozoc@cnio.es - github.com/fpozoc

Contributing

1. Fork it (https://github.com/fpozoc/advanced-bioinformatics-course).
2. Create your feature branch (git checkout -b feature/fooBar).
3. Commit your changes (git commit -am 'Add some fooBar').
4. Push to the branch (git push origin feature/fooBar).
5. Create a new Pull Request.