ROPES summer school - CRG - May 2023

GitHub repository

Contents:

• About the course
  • Outline
  • Learning objectives
  • Prerequisite / technical requirements
  • Dates, time, location
  • Program
• Introduction to Linux
  • What is Linux?
  • What is a Command Line Interface (GUI)?
  • Create directory and practice moving around
  • Download files from repositories
  • Manipulate files, piping, parsing, reformatting
  • Sequence file formats: Fasta and fastq
  • Bed format and regular expressions
  • Space in volumes and permissions
• Containers
  • Linux containers
  • Docker
  • Singularity
• Nextflow
  • What is Nextflow?
  • What is Nextflow for?
  • Main advantages
  • Workflow structure
  • Installation
  • Channels and Operators
  • Exercise
  • Processes
  • Workflow
• Master of Pores 2
  • Basics of Direct RNA Sequencing (DRS)
  • Master Of Pores 2 (MOP2) - preprocessing and polyA tail estimation (1)
  • Hands-on 1: mop_preprocess and mop_tail
  • Master Of Pores 2 (MOP2) - RNA modification detection (2)
  • Hands-on 2: mop_mod and mop_consensus