Course on Unix and work with genomic data - Prague, November 2021

This course is taught regularly as a subject 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 26.11.2021 (14.00-18.00)
Afternoon	Course Intro Introduction to Unix Basics of Unix
Saturday 27.11.2021 (10.00-18.00)
Morning	Genomic data Processing of plain text files in Unix
Lunch Break (~ 1h)
Afternoon	Project management in Unix Graphics Session
Sunday 28.11.2021 (10.00-18.00)
Morning	Read Quality Assembly
Lunch Break (~ 1h)
Afternoon	Bioinformatic pipelines Variant quality exercise

Initial instructions:

• Installation instructions
• Connecting to the remote machine

Course outline:

• Session 1: Basic Unix
  • Basic orientation
  • Installing software
  • Exercise
• Session 2: Genomic data
  • Common genomic 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: Unix - “Real” Project
  • Keep your stuff ordered
  • awk (pronounced [auk])
  • Functions in the Shell
  • Shell Scripts
  • Code management and sharing via GIT
  • Multi-file, multi-core processing
• Session 5: Graphics session
  • Summarization
  • Now open RStudio
  • Tidy data
• Session 6: Read quality
  • Phred encoding
  • FastQC
  • Parsing Fastq and decoding Phred
  • Quality by position
  • FastQC exercise
• Session 7: Genome assembly
• Session 8: Bioinformatic pipelines
  • Mouse Gene Ontology enrichment analysis pipeline
• Session 9: Variant quality

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