Course on Unix and work with genomic data - Prague, November 2023

This course takes place regularly in the winter term at the Department of Zoology, Faculty of Science, Charles University in Prague (MB170C47).

The aim of the course is to introduce the participants to Unix - an interface that is one of the most convenient options for working with big data in text formats. Special attention is given to working with Next Generation Sequencing (NGS) data. Most of the NGS data formats are intentionally text-based because the authors wanted to use Unix for most of the processing. Like that they can focus on the real problem they’re solving without having to program special tools for the mundane tasks, which can all be handled by combining basic Unix tools.

We’ll be using Slack ‘UNIX and NGS’ to share your login credentials and further info - use (this link to join).

Schedule:

Friday 24.11.2023 (14.00-18.00)
Afternoon	Course Intro Introduction to Unix Basics of Unix
Saturday 25.11.2023 (9.00-17.00)
Morning	Genomics data Processing of plain text files in Unix
Lunch Break (1.5h)
Afternoon	Running a project in Unix Graphics Session
Sunday 26.11.2023 (9.00-17.00)
Morning	Introduction to Git Variant quality exercise
Lunch Break (1.5h)
Afternoon	Bioinformatic pipelines Working remotely in the cloud

Initial instructions:

• Installation instructions
• Connecting to the remote machine

Course outline:

• Session 1: Basic Unix
  • Basic orientation
  • Installing software
  • Exercise
• Session 2: Genomics data
  • Common genomics tools
  • Standard genomic data formats
• Session 3: Plain text file processing in Unix
  • Pattern search & regular expressions
  • Word and line count
  • Retrieve & count unique records
  • String extraction and replacement
  • Join & paste data
  • Exercise
• Session 4: Running a project
  • Keep your stuff ordered
  • awk (pronounced [auk])
  • Functions in the Shell
  • Shell Scripts
  • Process multiple files
  • Scale up to multiple cores
• Session 5: Graphics session
  • Summarization
  • Visualize data in RStudio
  • Tidy data
• Session 6: Git and GitHub
  • Configure git
  • Create a local repository
  • Upload repository to GitHub
  • git commands: Basics
  • git commands: Branches
  • git commands: Merge
• Session 7: Variant quality
  • Extra R task
• Session 8: Bioinformatic pipelines
  • Mouse Gene Ontology enrichment analysis pipeline

Additional reference materials:

• Links
• A few more tips
• Reference manual for Unix introduction
• Important NGS formats
• Additional exercises

Supplemental information:

• Course materials preparation
• Slide decks